bayes error filter removes all INDELs

[ian1roberts]

May be I've misunderstood how the filter works, so might be my application error rather than a real issue.
Essentially, miseq amplicon data processed through GATK pipeline, calling glm=BOTH generates VCF that contains some nice INDELs

Post filtering thus ...

vcf_filter.py --site-quality=99 --genotype-quality=99 --eblr=-10  gatk_raw.vcf sq mgq eb > gatk_filtered.vcf

Contains no INDELs. I thought about it, and wondered if its appropriate to apply this filter to INDELs in tumour samples where the distribution of allele depths isn't expected to be negative binomial. So I added an argument to the filter to exclude it from variants typed INDEL

I hacked the ErrorBiasFilter to include the extra argparse:

parser.add_argument('--no-indels', type=bool, default=True,
                help='Apply filter to SNPs only')

and in init

self.no_indels = args.no_indels

and in call

if self.no_indels and record.is_indel:
            return None

Wanted to know if this is useful before I commit, or have I missed how this filter should work. Thanks, Ian