Filter out reads with several variants

[david.tamborero]

Hello everyone,

I am interested in filtering out those reads containing several misalignements with the reference genome, so such reads are not taken into account when looking for variants (for instance, not to take into account reads with more than 3 SNP and/or indels).

I am working with bfast + GATK recalibration/indel_realigner to obtain the bam, and samtools mpileup + varscan to perform the subsequent somatic variant call.

thanks for any help!
cheers
david