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brentp / vcfanno

annotate a VCF with other VCFs/BEDs/tabixed files
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0973-5
MIT License
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Does VCF anno strip FORMAT and GT fields after running? #8

Closed indapa closed 8 years ago

indapa commented 9 years ago

I ran vcfanno on NA12878 for a small region. The FORMAT and GT fields are stripped in the result file. Is this the desired behavior of the software? Here is before decoration:

chr22   42128241        .       CT      C       0       PASS    metal=platinum;isaac2=HD:0,LOOHD:0;bwa_freebayes=HD:0,LOOHD:0;bwa_platypus=HD:0,LOOHD:0;bwa_gatk3=HD:0,LOOHD:0;dist2closest=452 GT      0|1

Here is after:

chr22   42128241        .       CT      C       0.0     PASS    metal=platinum;isaac2=HD:0,LOOHD:0;bwa_freebayes=HD:0,LOOHD:0;bwa_platypus=HD:0,LOOHD:0;bwa_gatk3=HD:0,LOOHD:0;dist2closest=452;RSID=rs35742686;CYPALLELE=*3;HGVSc=NM_000106.5:c.2549delA
brentp commented 9 years ago

I didn't see this til now. I'll have this fixed for 0.8 release.

indapa commented 9 years ago

Great! Thank you! I'll check it out.

brentp commented 9 years ago

Hi @indapa I've updated this can you test if this executable addresses your problem: https://www.chpc.utah.edu/~u6000771/vcfanno_08a1 it's for 64bit linux

brentp commented 9 years ago

did this work for you?