VCF file is malformed while running gatk SelectVariants

Question

[luckysardar171]

Hello I am running GATK Selectvariant getting below error my code looking as below can anyone help resolve my error I think there is problem with my VCF file not able rectify what is wrong with vcf file.

my sample vcf file enter link description here

gatk SelectVariants -select-type SNP -R Reference_genome.fa -V test.vcf.gz -O tmp.vcf -sn FVB_NJ

error htsjdk.tribble.TribbleException: The provided VCF file is malformed at approximately line number 143: 0 is an invalid filter name in vcf4,

Answer 1

[Pierre Lindenbaum]

line 143 is:

1   3000020 .   T   A   377 SnpGap;MinAB;MinABF;MinABR;MinGQ;MinDP  DP=152;ADF=0,151;ADR=0,0;AD=0,151;VDB=0;SGB=-6.39018;MQ0F=0.0986842;AC=80;AN=80;DP4=0,0,152,0;MQ=28;CSQ=A||||intergenic_variant|||||||||||  GT:PL:DP:SP:ADF:ADR:AD:GQ:FT    1/1:6,9,0:4:0:0,3:0,0:0,3:127:0 1/1:12,15,0:5:0:0,5:0,0:0,5:127:0   (....)

your gentypes are FILTERED with FORMAT/FT

your VCF is version 4.2

##fileformat=VCFv4.2

but using 0 instead of PASS for the value of FORMAT/FT is not allowed because it looks like you're using an old specification. That's why you get this message:0 is an invalid filter name in vcf4

Your file was generated with the old ##samtoolsVersion=samtoolsVersion=1.6+htslib-1.6 which was written in 2017. Update your tools.

[hemantcnaik]

Thanks for the ansr, Is there any way I can resolve this problem if I remove FORMAT/FT from VCF file it will create any problem or if I fill replace zero with PASS. is there any tool I want just GT and DP fileld

[Pierre Lindenbaum]

you can try to remove the attribute with bctools annotate -x 'FORMAT/FT' input.vcf.gz

[Pierre Lindenbaum]

but again, you're working with old tools...

[luckysardar171]

Okay I will update my tools, if I use the current VCF file is it okay to proceed I need GT information from VCF file