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somatico_google_colab.ipyhb
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somatico_google_colab.ipyhb
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{
"nbformat": 4,
"nbformat_minor": 0,
"metadata": {
"colab": {
"name": "somatico-google-colab.ipynb",
"provenance": [],
"collapsed_sections": [
"E0nW4L4AYdZk",
"nC_6PrtPZCyH"
]
},
"kernelspec": {
"name": "python3",
"display_name": "Python 3"
},
"language_info": {
"name": "python"
}
},
"cells": [
{
"cell_type": "markdown",
"metadata": {
"id": "ah_iV1YQMqrC"
},
"source": [
"# Workflow\n",
"Os arquivos BA (tumor e normal) já foram gerados e estão prontos para a chamada de variates (ver Anexo 1). Então, agora vamos fazer download da referência chr9 e gerar o index com o programa samtools."
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "tBDLyVs9MeIq"
},
"source": [
"##Clonar Repositório \n",
"> github.com/renatopuga/somatico"
]
},
{
"cell_type": "code",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "Q6RwxVgfMUZP",
"outputId": "3ee823c7-6e74-4559-a891-bc23f014308c"
},
"source": [
"!git clone https://github.com/renatopuga/somatico.git"
],
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Cloning into 'somatico'...\n",
"remote: Enumerating objects: 72, done.\u001b[K\n",
"remote: Counting objects: 100% (72/72), done.\u001b[K\n",
"remote: Compressing objects: 100% (71/71), done.\u001b[K\n",
"remote: Total 72 (delta 31), reused 0 (delta 0), pack-reused 0\u001b[K\n",
"Unpacking objects: 100% (72/72), done.\n"
]
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "HPpmO49BMlHC"
},
"source": [
"##Preparando a Referência - chr9\n",
"Os arquivos BAM que vamos utilizar não contém os carateres `chr` no cabeçalho. Ex.: `>9`.\n",
"O arquivo que vamos fazer download `chr9.fa.gz` tem o cabeçalho `>chr9`, então precisaremos alterar essa parte para não termos erro de contigs quando rodar o GATK. Leia mais sobre [*missing or incompatible contigs*](https://gatk.broadinstitute.org/hc/en-us/articles/360035891131-Errors-about-input-files-having-missing-or-incompatible-contigs)"
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "7lIUlFw3OOmU"
},
"source": [
"### Download chr9.fa.gz\n",
"> `wget -c` faz download e resume o arquivo se necessário."
]
},
{
"cell_type": "code",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "QKxpV4KCNBHL",
"outputId": "cb70ce9a-582c-4523-a9fd-f0fdb2fa6392"
},
"source": [
"!wget -c https://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/chr9.fa.gz"
],
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"--2021-09-22 01:52:33-- https://hgdownload.soe.ucsc.edu/goldenPath/hg19/chromosomes/chr9.fa.gz\n",
"Resolving hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)... 128.114.119.163\n",
"Connecting to hgdownload.soe.ucsc.edu (hgdownload.soe.ucsc.edu)|128.114.119.163|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 39464200 (38M) [application/x-gzip]\n",
"Saving to: ‘chr9.fa.gz’\n",
"\n",
"chr9.fa.gz 100%[===================>] 37.64M 12.2MB/s in 3.2s \n",
"\n",
"2021-09-22 01:52:37 (11.6 MB/s) - ‘chr9.fa.gz’ saved [39464200/39464200]\n",
"\n"
]
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "qC1Cy2oROiIc"
},
"source": [
"### Alterar nome do cabeçaho do arquivo FASTA\n",
"> DE: `>chr9` para `>9`"
]
},
{
"cell_type": "code",
"metadata": {
"id": "LVT_9ZneOvrO"
},
"source": [
"!zcat chr9.fa.gz | sed -e \"s/chr//g\" > chr9.fa"
],
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {
"id": "o1YUuqyYO-X0"
},
"source": [
"### Verificar a Mudança: comando `head`\n",
"> `head` lê as dez primeiras linhas de um arquivo"
]
},
{
"cell_type": "code",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "tN94DhxmPNRB",
"outputId": "eeb97dc0-7ce3-41ac-fc92-eb5a73630e9a"
},
"source": [
"!head chr9.fa"
],
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
">9\n",
"NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n",
"NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n",
"NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n",
"NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n",
"NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n",
"NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n",
"NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n",
"NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n",
"NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n"
]
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "31sFUWrQPgLn"
},
"source": [
"## samtools\n",
"Samtools é um conjunto de programas para interagir com dados de sequenciamento de alto rendimento."
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "P1_BYxSFQN63"
},
"source": [
"### Instalar samtools"
]
},
{
"cell_type": "code",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "m8I2keRePy4w",
"outputId": "f9da4348-6479-4d13-94ed-05f6bb1d4330"
},
"source": [
"!sudo apt-get install samtools "
],
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Reading package lists... Done\n",
"Building dependency tree \n",
"Reading state information... Done\n",
"The following additional packages will be installed:\n",
" cwltool libc-ares2 libhts2 libjs-bootstrap nodejs nodejs-doc\n",
" python-asn1crypto python-avro python-cachecontrol python-certifi\n",
" python-cffi-backend python-chardet python-cryptography python-enum34\n",
" python-html5lib python-idna python-ipaddress python-isodate python-lockfile\n",
" python-mistune python-openssl python-pkg-resources python-pyparsing\n",
" python-rdflib python-rdflib-jsonld python-requests python-ruamel.yaml\n",
" python-schema-salad python-shellescape python-six python-sparqlwrapper\n",
" python-typing python-urllib3 python-webencodings\n",
"Suggested packages:\n",
" python-cryptography-doc python-cryptography-vectors python-enum34-doc\n",
" python-genshi python-lxml python-lockfile-doc python-openssl-doc\n",
" python-openssl-dbg python-setuptools python-pyparsing-doc python-rdflib-doc\n",
" python-rdflib-tools python-socks python-ntlm\n",
"The following NEW packages will be installed:\n",
" cwltool libc-ares2 libhts2 libjs-bootstrap nodejs nodejs-doc\n",
" python-asn1crypto python-avro python-cachecontrol python-certifi\n",
" python-cffi-backend python-chardet python-cryptography python-enum34\n",
" python-html5lib python-idna python-ipaddress python-isodate python-lockfile\n",
" python-mistune python-openssl python-pkg-resources python-pyparsing\n",
" python-rdflib python-rdflib-jsonld python-requests python-ruamel.yaml\n",
" python-schema-salad python-shellescape python-six python-sparqlwrapper\n",
" python-typing python-urllib3 python-webencodings samtools\n",
"0 upgraded, 35 newly installed, 0 to remove and 37 not upgraded.\n",
"Need to get 8,568 kB of archives.\n",
"After this operation, 41.0 MB of additional disk space will be used.\n",
"Get:1 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-pkg-resources all 39.0.1-2 [128 kB]\n",
"Get:2 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-six all 1.11.0-2 [11.3 kB]\n",
"Get:3 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-isodate all 0.6.0-1 [23.8 kB]\n",
"Get:4 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-pyparsing all 2.2.0+dfsg1-2 [52.1 kB]\n",
"Get:5 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-rdflib all 4.2.1-2 [237 kB]\n",
"Get:6 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-certifi all 2018.1.18-2 [144 kB]\n",
"Get:7 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-chardet all 3.0.4-1 [80.3 kB]\n",
"Get:8 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-idna all 2.6-1 [32.4 kB]\n",
"Get:9 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 python-urllib3 all 1.22-1ubuntu0.18.04.2 [86.0 kB]\n",
"Get:10 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 python-requests all 2.18.4-2ubuntu0.1 [58.5 kB]\n",
"Get:11 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-ruamel.yaml amd64 0.15.34-1 [183 kB]\n",
"Get:12 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-cachecontrol all 0.11.7-1 [15.2 kB]\n",
"Get:13 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-lockfile all 1:0.12.2-2 [14.6 kB]\n",
"Get:14 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-mistune all 0.8.3-2 [13.8 kB]\n",
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"Get:16 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-typing all 3.6.2-1 [22.2 kB]\n",
"Get:17 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-avro all 1.8.2+dfsg-1 [23.2 kB]\n",
"Get:18 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libjs-bootstrap all 3.3.7+dfsg-2 [228 kB]\n",
"Get:19 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-schema-salad all 2.6.20171201034858-3 [260 kB]\n",
"Get:20 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-shellescape all 3.4.1-2 [4,432 B]\n",
"Get:21 http://archive.ubuntu.com/ubuntu bionic/universe amd64 cwltool all 1.0.20180302231433-1 [143 kB]\n",
"Get:22 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libhts2 amd64 1.7-2 [300 kB]\n",
"Get:23 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 nodejs-doc all 8.10.0~dfsg-2ubuntu0.4 [752 kB]\n",
"Get:24 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-asn1crypto all 0.24.0-1 [72.7 kB]\n",
"Get:25 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-cffi-backend amd64 1.11.5-1 [63.4 kB]\n",
"Get:26 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-enum34 all 1.1.6-2 [34.8 kB]\n",
"Get:27 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-ipaddress all 1.0.17-1 [18.2 kB]\n",
"Get:28 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 python-cryptography amd64 2.1.4-1ubuntu1.4 [276 kB]\n",
"Get:29 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-webencodings all 0.5-2 [10.3 kB]\n",
"Get:30 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-html5lib all 0.999999999-1 [83.6 kB]\n",
"Get:31 http://archive.ubuntu.com/ubuntu bionic/main amd64 python-openssl all 17.5.0-1ubuntu1 [41.3 kB]\n",
"Get:32 http://archive.ubuntu.com/ubuntu bionic/universe amd64 python-sparqlwrapper all 1.7.6-2 [21.8 kB]\n",
"Get:33 http://archive.ubuntu.com/ubuntu bionic/universe amd64 samtools amd64 1.7-1 [288 kB]\n",
"Get:34 http://archive.ubuntu.com/ubuntu bionic-updates/main amd64 libc-ares2 amd64 1.14.0-1ubuntu0.1 [37.5 kB]\n",
"Get:35 http://archive.ubuntu.com/ubuntu bionic-updates/universe amd64 nodejs amd64 8.10.0~dfsg-2ubuntu0.4 [4,796 kB]\n",
"Fetched 8,568 kB in 0s (33.5 MB/s)\n",
"debconf: unable to initialize frontend: Dialog\n",
"debconf: (No usable dialog-like program is installed, so the dialog based frontend cannot be used. at /usr/share/perl5/Debconf/FrontEnd/Dialog.pm line 76, <> line 35.)\n",
"debconf: falling back to frontend: Readline\n",
"debconf: unable to initialize frontend: Readline\n",
"debconf: (This frontend requires a controlling tty.)\n",
"debconf: falling back to frontend: Teletype\n",
"dpkg-preconfigure: unable to re-open stdin: \n",
"Selecting previously unselected package python-pkg-resources.\n",
"(Reading database ... 155013 files and directories currently installed.)\n",
"Preparing to unpack .../00-python-pkg-resources_39.0.1-2_all.deb ...\n",
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"update-alternatives: using /usr/bin/nodejs to provide /usr/bin/js (js) in auto mode\n",
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"/sbin/ldconfig.real: /usr/local/lib/python3.7/dist-packages/ideep4py/lib/libmkldnn.so.0 is not a symbolic link\n",
"\n",
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]
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "jCUrG6fyQjch"
},
"source": [
"### samtools faidx\n",
"> index/extract FASTA\n",
"Input é o arquivo `chr9.fa` e o ouput o arquivo `chr9.fa.fai`."
]
},
{
"cell_type": "code",
"metadata": {
"id": "apQ0oH3qQpgw"
},
"source": [
"!samtools faidx chr9.fa"
],
"execution_count": null,
"outputs": []
},
{
"cell_type": "markdown",
"metadata": {
"id": "5HTNIwrLQ-xe"
},
"source": [
"## Genome Analysis Toolkit - GATK4\n",
"> Version: 4.2.2.0\n",
"\n",
"Genome Analysis Toolkit - Variant Discovery in High-Throughput Sequencing Data. https://gatk.broadinstitute.org/\n",
"\n",
"### Download"
]
},
{
"cell_type": "code",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "ol3ZG5-mRPlP",
"outputId": "667b76f8-fad6-473b-f26b-d9fb23a1111f"
},
"source": [
"!wget -c https://github.com/broadinstitute/gatk/releases/download/4.2.2.0/gatk-4.2.2.0.zip"
],
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"--2021-09-22 02:10:48-- https://github.com/broadinstitute/gatk/releases/download/4.2.2.0/gatk-4.2.2.0.zip\n",
"Resolving github.com (github.com)... 140.82.121.4\n",
"Connecting to github.com (github.com)|140.82.121.4|:443... connected.\n",
"HTTP request sent, awaiting response... 302 Found\n",
"Location: https://github-releases.githubusercontent.com/27452807/0147a07c-fbe2-4017-96dc-7885874c9484?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210922%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210922T021049Z&X-Amz-Expires=300&X-Amz-Signature=889e5895e5beabcd6ecc446c1a4e5b2da12ca4abf8ca26494c6cfac642cecf85&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=27452807&response-content-disposition=attachment%3B%20filename%3Dgatk-4.2.2.0.zip&response-content-type=application%2Foctet-stream [following]\n",
"--2021-09-22 02:10:49-- https://github-releases.githubusercontent.com/27452807/0147a07c-fbe2-4017-96dc-7885874c9484?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAIWNJYAX4CSVEH53A%2F20210922%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20210922T021049Z&X-Amz-Expires=300&X-Amz-Signature=889e5895e5beabcd6ecc446c1a4e5b2da12ca4abf8ca26494c6cfac642cecf85&X-Amz-SignedHeaders=host&actor_id=0&key_id=0&repo_id=27452807&response-content-disposition=attachment%3B%20filename%3Dgatk-4.2.2.0.zip&response-content-type=application%2Foctet-stream\n",
"Resolving github-releases.githubusercontent.com (github-releases.githubusercontent.com)... 185.199.110.154, 185.199.111.154, 185.199.109.154, ...\n",
"Connecting to github-releases.githubusercontent.com (github-releases.githubusercontent.com)|185.199.110.154|:443... connected.\n",
"HTTP request sent, awaiting response... 200 OK\n",
"Length: 475027366 (453M) [application/octet-stream]\n",
"Saving to: ‘gatk-4.2.2.0.zip’\n",
"\n",
"gatk-4.2.2.0.zip 100%[===================>] 453.02M 56.7MB/s in 11s \n",
"\n",
"2021-09-22 02:11:00 (42.2 MB/s) - ‘gatk-4.2.2.0.zip’ saved [475027366/475027366]\n",
"\n"
]
}
]
},
{
"cell_type": "markdown",
"metadata": {
"id": "ZJH73Nv9Rg_9"
},
"source": [
"### Descompactar\n",
"> comando `unzip`"
]
},
{
"cell_type": "code",
"metadata": {
"colab": {
"base_uri": "https://localhost:8080/"
},
"id": "bqSkBSJ0RZnH",
"outputId": "28707da3-d7d7-487a-82bc-c3bc2c7152fe"
},
"source": [
"!unzip gatk-4.2.2.0.zip"
],
"execution_count": null,
"outputs": [
{
"output_type": "stream",
"name": "stdout",
"text": [
"Archive: gatk-4.2.2.0.zip\n",
" creating: gatk-4.2.2.0/\n",
" creating: gatk-4.2.2.0/gatkdoc/\n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_rnaseq_ASEReadCounter.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_analysis_replicates_CollectIndependentReplicateMetrics.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_dragstr_CalibrateDragstrModel.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_annotator_ChromosomeCounts.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_engine_filters_LibraryReadFilter.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_vqsr_FilterVariantTranches.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_analysis_CollectWgsMetricsWithNonZeroCoverage.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_engine_filters_ReadFilterLibrary$NonChimericOriginalAlignmentReadFilter.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_analysis_MeanQualityByCycle.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_illumina_quality_CollectHiSeqXPfFailMetrics.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_spark_pipelines_PrintReadsSpark.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_vcf_GenotypeConcordance.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_sam_CheckTerminatorBlock.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_engine_filters_ReadLengthReadFilter.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_qc_Pileup.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_engine_filters_OverclippedReadFilter.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_sam_CleanSam.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_mutect_CreateSomaticPanelOfNormals.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_arrays_GtcToVcf.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_qc_CheckPileup.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_BwaMemIndexImageCreator.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_annotator_OrientationBiasReadCounts.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_vcf_RenameSampleInVcf.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_ReadAnonymizer.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_engine_filters_ReadFilterLibrary$MappingQualityAvailableReadFilter.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_annotator_CountNs.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_annotator_AssemblyComplexity.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_analysis_CollectOxoGMetrics.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_engine_filters_ReadFilterLibrary$NotProperlyPairedReadFilter.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_fasta_FastaReferenceMaker.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_engine_filters_WellformedReadFilter.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_annotator_AlleleFraction.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_spark_pipelines_metrics_QualityScoreDistributionSpark.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_annotator_DepthPerSampleHC.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_engine_filters_SampleReadFilter.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_bqsr_AnalyzeCovariates.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_annotator_RMSMappingQuality.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_engine_filters_ReadFilterLibrary$FirstOfPairReadFilter.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_analysis_artifacts_ConvertSequencingArtifactToOxoG.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_spark_pipelines_CountBasesSpark.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_spark_pipelines_CountReadsSpark.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_funcotator_Funcotator.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_analysis_CollectQualityYieldMetrics.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_copynumber_CreateReadCountPanelOfNormals.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_spark_pathseq_PathSeqPipelineSpark.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_spark_sv_evidence_CalcMetadataSpark.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_engine_filters_ReadFilterLibrary$SecondOfPairReadFilter.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_engine_filters_AlignmentAgreesWithHeaderReadFilter.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_sam_markduplicates_CollectDuplicateMetrics.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_annotator_allelespecific_AS_StrandOddsRatio.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_vcf_filter_FilterVcf.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_spark_ParallelCopyGCSDirectoryIntoHDFSSpark.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_fasta_ShiftFasta.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_tools_walkers_varianteval_VariantEval.html \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_analysis_CollectRrbsMetrics.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/picard_vcf_MendelianViolations_FindMendelianViolations.json \n",
" inflating: gatk-4.2.2.0/gatkdoc/org_broadinstitute_hellbender_engine_filters_ReadFilterLibrary$NotSecondaryAlignmentReadFilter.json \n",
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