How to sort vcf file
1
0
Entering edit mode
8 months ago

Here is a screenshot of my VCF and I want to extract info from an extra column put in each value in a separate column like a standard VCF file!

Thanks in advance!

vcf • 826 views
ADD COMMENT
2
Entering edit mode
8 months ago

the correct answer would be

bcftools sort your.vcf

but your image shows that it is not a VCF file. The last VCF header should be #CHROM POS ID REF ALT QUAL FILTER INFO... so It's something else... with a VCF header (##).

and the usual associated image:

enter image description here

ADD COMMENT
0
Entering edit mode

yeah! The VCF file is annotated with 1)snpEff and 2)VEP (variant effect predictor). Now I want to separate the fields. !!!

ADD REPLY
0
Entering edit mode

Now I want to separate the fields. !!!

? that's not sorting a vcf

ADD REPLY
0
Entering edit mode

I mean extract the fields. and it's not a proper VCF cause this is generated by VEP (ensemble).

ADD REPLY

Login before adding your answer.

Traffic: 2841 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6