You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Currently, the only supported merge strategy is MOVE_TO_CALLS, which only merges samples that have the exact reference_name:start_position:end_position:reference_bases:alternate_bases.
For gVCF files, we like to add 0/0 to samples that don't have a variant. For instance, "sample1" has a non-variant from position 1-100, "sample2" has a variant 1/0 in position 55. We should output a single row at position 55 for both "sample1" and "sample2" that has 0/0 and 1/0 for "sample1" and "sample2", respectively.
We currently have a merging logic for gVCF files (merge_with_non_variants_strategy.py). It can handle non-variants, but needs to be cleaned up and tested further. It also depends on a fix in the intervaltree library (see chaimleib/intervaltree#63).
This task is only for supporting merging SNPs with non-variants.
The text was updated successfully, but these errors were encountered:
Currently, the only supported merge strategy is MOVE_TO_CALLS, which only merges samples that have the exact
reference_name:start_position:end_position:reference_bases:alternate_bases
.For gVCF files, we like to add
0/0
to samples that don't have a variant. For instance, "sample1" has a non-variant from position 1-100, "sample2" has a variant1/0
in position 55. We should output a single row at position 55 for both "sample1" and "sample2" that has0/0
and1/0
for "sample1" and "sample2", respectively.We currently have a merging logic for gVCF files (merge_with_non_variants_strategy.py). It can handle non-variants, but needs to be cleaned up and tested further. It also depends on a fix in the intervaltree library (see chaimleib/intervaltree#63).
This task is only for supporting merging SNPs with non-variants.
The text was updated successfully, but these errors were encountered: