Read depth lost after merging

[ch...@cornell.edu]

Hi,

I ran the command below on two vcf files, which both contain depth information, to merge them, do some site filtering, and then export the merged file.

run_pipeline.pl -fork1  -vcf vcf1.vcf -fork2 -vcf vcf2.vcf -combine3  -input1 -input2 \

-mergeGenotypeTables \

-FilterSiteBuilderPlugin -siteMinCount 300 -endPlugin \

-export merged.vcf -exportType VCF

It seems to be working correctly, except that the resulting merged.vcf file no longer contains depth info. Is there a way to preserve the depth information in the output file? Tassel version is 5.2.48.

Thanks,

Chris

[Terry Casstevens]

That is a limitation of the -mergeGenotypeTables function. Handling
merging comprehensively has been challenging. My hope is to address
this in the future but it's not a short term fix.

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[ch...@cornell.edu]

Okay, good to know. Thanks.

Chris