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filtering a VCF file

I have a VCF file which I have filtered using grep command for various flags/ tags. The file is very small around 10000 rows.I can easily open in any txt editor or excel.

Here are few lines:

1    14662255    .    CAG    GAG,C    .    .    NS=2;AN=4;AC=2,1;CGA_XR=.,dbsnp.126|rs34561318;CGA_RPT=(GA)n|Simple_repeat|0.0    GT:PS:SS:FT:GQ:HQ:EHQ:CGA_CEHQ:GL:CGA_CEGL:DP:AD:CGA_RDP:CGA_ODP:CGA_OAD:CGA_ORDP:CGA_SOMC:CGA_SOMR:CGA_SOMS:CGA_SOMF    1|0:14662255:.:PASS:63:63,287:62,276:14,52:-63,0,-287,-63,-287,-287:-14,0,-52,-14,-52,-52:31:7,24:24:27:13,14:14:.:.:.:.    1|2:14662255:Somatic:SQLOW;FET30:170:170,170:167,167:47,49:-170,-170,-170,-170,0,-170:-49,-49,-49,-47,0,-47:34:21,14:21:34:15,23:23:del:0.146:-17:0
1    17299453    .    TA    T,AA    .    .    NS=2;AN=4;AC=1,1;CGA_FI=9696|NM_014675.3|CROCC|UTR3|UNKNOWN-INC,9696|NM_014675.3|CROCC|UTR3|UNKNOWN-INC    GT:PS:SS:FT:GQ:HQ:EHQ:CGA_CEHQ:GL:CGA_CEGL:DP:AD:CGA_RDP:CGA_ODP:CGA_OAD:CGA_ORDP:CGA_SOMC:CGA_SOMR:CGA_SOMS:CGA_SOMF    1/0:.:.:PASS:51:51,535:0,485:0,45:-51,0,-535,-51,-535,-535:0,0,-45,0,-45,-45:68:5,53:53:47:1,43:43:.:.:.:.    2/0:.:Somatic:SQLOW;FET30:66:66,348:0,279:0,52:-66,-66,-348,0,-348,-348:0,0,-52,0,-52,-52:44:7,37:37:59:2,56:56:snp:0.012:-20:14

Now I would like to filter for gene names / word (say FET20) Can I do it now non programmatically in a GUI tool or Excel . I see there is information of genotypes which I cannot handle in excel and the columns with multiple types of information.

Is there any easy way of handling filtering these small datasets.

Thanks

vcf-filtering
• 4,352 views • link
updated by Ram Ram • written by kanwarjag kanwarjag

Given the amount of monkeying around you'd probably need to do, why bother? This sounds like a simple job for grep or awk.

• 0 views • link
written by Devon Ryan Devon Ryan

The problem is when I use two filters like grep A:B it looses VCF format. Is there a way to mainatin a standard VCF format after grep. The VCF format will allow me to annotate my variation calls in any other standard tool.

• 0 views • link
updated by Ram Ram • written by kanwarjag kanwarjag

2 answers

The suggestions to use grep are good, and a two step grep will maintain the VCF header in your output for downstream processing:

grep ^# orig.vcf > filtered.vcf
grep -v ^# orig.vcf | grep FET20 >> filtered.vcf
• 0 views • link
updated by Ram Ram • written by Brad Chapman Brad Chapman

You can use "SnpSift filter" for filtering VCF files. But if the filter requirement is so simple, grep can do the trick as well...

• 0 views • link
updated by Ram Ram • written by Pablo Pablo

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