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hard filtering one WGS raw.g.vcf


Im trying to apply hard filter to one WGS.g.vcf (coming form HaplotypeCaller).
The command im using is:
java -jar ${GATK}/GenomeAnalysisTK.jar -R ${reference}/mm10.fa -T SelectVariants -V ${variant}/mouseWGS.g.vcf -selectType SNP -o ${output}/my_mouse.vcf

It produce a "my_mouse.vcf" file with only the vcf header (no SNP entries).
When checking the log file there are non warnings and at the end it looks like:

INFO 16:50:56,991 ProgressMeter - chrY:53156701 2.690567022E9 3.3 h 4.0 s 98.5% 3.3 h 2.9 m
INFO 16:51:26,992 ProgressMeter - chrY_JH584301_random:230401 2.729494067E9 3.3 h 4.0 s 100.0% 3.3 h 4.0 s
INFO 16:51:28,959 SelectVariants - 689216856 records processed.
INFO 16:51:28,997 ProgressMeter - done 2.730871774E9 3.3 h 4.0 s 100.0% 3.3 h 0.0 s

INFO 16:51:28,998 ProgressMeter - Total runtime 11762.70 secs, 196.04 min, 3.27 hours

Done. There were no warn messages.

the GATK version im using is: GATK v3.8-0-ge9d806836
I have checked the memory and it is enough; morover, I have tried different options (--selectTypeToInclude SNP, or --selectTypeToExclude INDEL) but getting the same thing, no warnings and no SNPs....Would you please help me in understanding what is wrong?

Thanks a lot in advance for your support,

Best Answer


  • lbuggiottilbuggiotti Member

    Hi Sheila,

    SelectVariants worked on the vcf generated with GenotypeGVCF...i thought that it wouldn't be necessary when working with only one whole genome sequence.
    Thanks a lot for your help,


  • SheilaSheila Broad InstituteMember, Broadie ✭✭✭✭✭

    Hi Laura,

    The GVCFs are not supposed to be used in final analysis. They are meant to be an intermediate file in the GVCF workflow. Glad to hear your issue is solved :smile:


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