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Some SNV genome variants were found outside of --target_bed file with --bait_padding #631
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Thanks for reporting this sitems! I am working on a fix here #633 |
Have a new issue with running DeepVariant on exomes after the merge of PR #633.
Looks like the call regions should be defined using bed file format and not interval_list format. Running the deepvariant help command:
What do you think about using the bed file supplied with the parameter |
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Description of the bug
Relevant portion of my --target_bed file looks like
chr1 35720 35736
chr1 69088 69970
chr1 138529 139696
I'm processing WES fastq file with '--target_bed and --bait_padding 500' options, but in outpur/call_snv/genome/output_snv.vcf.gz I see variants like this
chr1 88177 chr1_88177_G_C G C 8 . AF=1;AQ=8;FOUND_IN=deepvariant GT:DP:AD:GQ:PL:RNC 1/1:2:0,2:6:8,6,0:..
The variant is outside of any (padded) bed region.
Command used and terminal output
No response
Relevant files
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System information
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