about tools working on VCF and BAM files

Question

[Bogdan]

Dear all,

please could you advise on any tool that could take a VCF file and a BAM file and computes for each SNP or INDEL some MISSING FIELDS in the VCF file like STRAND BIAS, distribution of the reads on + and - strand, for reference and alternate allele, etc ?

thanks, and happy weekend !

-- bogdan

[GouthamAtla]

If you know a bit of scripting, you could use pysam and pysamstats to query any kind of information you need from a VCF and BAM file.

[Bogdan]

thanks, will look into it !

[Bogdan]

A tool like VariantAnnotator (from GATK package) would be helpful, although VariantAnnotator gives some errors for some variants.