Extract data from VCF file

Question

[inkprs]

How can I extract below fields from a VCF file?

I am looking for python parser for VCF file.

'ALLELE_CALL', 'IS_HETEROZYGOUS', 'NUM_READS', 'TOTAL_READ_DEPTH'

My VCF file looks like:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT MATERIAL1 MATERIAL2 MATERIAL..n

[Pierre Lindenbaum]

what are VARIANT_TYPE, SEQUENCE,ALLELE_CALL,VALUE, etc... ? How can we know what you want to put in those columns ?

[inkprs]

Updated the question.

Answer 1

[jzluo1]

They're probably in the INFO field. You can just use cut, or GATK VariantsToTable, or PyVCF. Lots of options!

Answer 2

[shenwei356]

Try @brentp 's cyvcf2 (cython + htslib == fast VCF and BCF processing), a fast python (2 and 3) parsing of VCF and BCF including region-queries, published on Bioinformatics.