genotypeFilterExpression not behaving as expected in VariantFiltration

I'm trying to filter at the sample level by the sample DP and I'm using the following commands on the toy file I made here. I expected a "lowdp" FT tag to be added to the the first sample in output.vcf because its DP is lower than 8, but instead I see no FT tag added. When I run the same commands on the second toy file where the locus-level DP is lower than 8 the FT tag gets added. But this is not the appropriate behavior is it? Am I doing something wrong? I tried my best to find an answer in previous posts but no luck.

java -Xmx1G -jar ../../bin/GenomeAnalysisTK-2.1-3-g8892c10/GenomeAnalysisTK.jar \
-T VariantFiltration \
-R ../../data/gsa_bundle_1.5/b37/human_g1k_v37.fasta \
--variant test.vcf \
-o test.output.vcf \
--genotypeFilterExpression "DP < 8 " \
--genotypeFilterName "lowDP"

java -Xmx1G -jar ../../bin/GenomeAnalysisTK-2.1-3-g8892c10/GenomeAnalysisTK.jar \
-T VariantFiltration \
-R ../../data/gsa_bundle_1.5/b37/human_g1k_v37.fasta \
--variant test.2.vcf \
-o test.output.2.vcf \
--genotypeFilterExpression "DP < 8 " \
--genotypeFilterName "lowDP"

test.vcf:

fileformat=VCFv4.1

FORMAT=<ID=DP,Number=1,Type=Integer,Description="">

FORMAT=<ID=GT,Number=1,Type=String,Description="".

INFO=<ID=DP,Number=1,Type=Integer,Description="">

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Test1 Test2

1 13504 . G A 93.93 . DP=50 GT:DP 0/0:5 0/0:50

test.output.vcf:
...

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Test1 Test2

1 13504 . G A 93.93 PASS DP=50 GT:DP 0/0:5 0/0:50

test.2.vcf:

fileformat=VCFv4.1

FORMAT=<ID=DP,Number=1,Type=Integer,Description="">

FORMAT=<ID=GT,Number=1,Type=String,Description="".

INFO=<ID=DP,Number=1,Type=Integer,Description="">

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Test1 Test2

1 13504 . G A 93.93 . DP=7 GT:DP 0/0:5 0/0:2

test.output.2.vcf:
...

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Test1 Test2

1 13504 . G A 93.93 PASS DP=7 GT:DP:FT 0/0:5:lowDP 0/0:2:lowDP

Best Answer

Answers

Sign In or Register to comment.