Filreing vcf files not giving any results

Question

[abdulbenissa]

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.

[victoria_aleks]

hi Abdul, did you solve the problem?:)

Answer 1

[willgilks]

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'.

[abdulbenissa]

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

[abdulbenissa]

sorry SamTools has been used to call the variants I have.

Answer 2

[willgilks]

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