Find mosaic variants.

Rules

• the parents have 0 alternate alleles
• the kid has >= 2 alternate alleles

These include sites where the kid is likely to be called as homozygous reference and would be missed with normal variant calling method.

Usage

python mosaic.py $region $ped $fasta $bams

e.g.

python mosaic.py 9:135766735-135820020 my.ped hs37d5.fa /path/to/*.bam

Requirements

• Samples names in the ped must match the read-groups in the bam.
• Freebayes must be installed
• peddy python module must be installed

This will only run on trios specified in the ped file. It will

It will output a VCF from freebayes with only candidate mosaic variants in any of the kids. It adds a MOSAIC field to the info that indicates which sample has evidence of mosaicism, and what are the ref and alt counts and what are the sum of alternate quality score, e.g.:

MOSAIC=sample_z42:114:3:33;...

where here, sample_z42 has 114 reference alleles and 3 alternate alles with a total sum quality of 33. So this candidate will likely be filtered downstream.

If there are multiple probands that are candidates for mosaicism at this site, they will be delimited by "|".