Okay I think I missing something here , the gVCF file I have header is
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
chr1 10352 . T TA 426 PASS CIGAR=1M1I;IDREP=2;REFREP=1;REGION=OFFTARGET;RU=A;SF=0,1,2 GT:GQ:GQX:DPI:AD 0/1:466:13:25:11,11
chr1 14907 . A G 232 LowGQXHetSNP REGION=;SF=0f,1,2;SNVHPOL=2;SNVSB=-26.4 GT:GQ:GQX:DP:DPF:AD 0/1:7:2:21:0:2,19
chr1 14930 . A G 241 PASS REGION=;SF=0,1,2;SNVHPOL=2;SNVSB=-30.6 GT:GQ:GQX:DP:DPF:AD 1/1:36:19:13:0:0,13
when I run the following command I have this error or a vcf files with header and no variants :
$> vcffilter -f "GQX > 30" A.vcf > A.filtered.vcf
$> vcffilter -f "DP > 10" A.vcf > A.filtered.vcf
$> vcffilter -f "QUAL > 30 " A.vcf > A.filtered.vcf
for example of the Error I have :
$> cannot compare (>) objects of dissimilar types
3 4
$ > Segmentation fault: 11
I know it can be done by some bash commands for example but I would like to keep the format as vcf.
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abdulbenissa •
Hi Abdul,
I don't know what program you're using but I've had a previous issue with jexel expressions like "GQX > 30" when using the GATK program. Basically, depending on what version of Linux you're using, you may have to remove the spaces, so "GQX>30", or change the speach marks, like GQX > 30 or 'GQX > 30'.
I have done the changes you recommended but it give this error
$> libc++abi.dylib: terminating with uncaught exception of type std::out_of_range: basic_string
Abort trap: 6
sorry SamTools has been used to call the variants I have.
I assume you are using bcftools for the filtering. In your vcf file are there any header rows above the column names? Did it give the libc++ error message for all the commands or just the first one? GXQ is a genotype field so maybe you have to specify that with a different command option, and not -f.
If you can use GATK instead, I have some code for filtering here https://zenodo.org/record/159272 code.zip, format_hcVcf.sh with more info here https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_filters_VariantFiltration.php
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hi Abdul, did you solve the problem?:)