ekg/freebayes — Issue #19: --no-mnps --no-complex  --use-best-n-alleles problems
Author: jamescasbon
Created: 2011-10-17 16:31:11+00:00
State: open

I have a good quality GG/TC MNP:

$ freebayes -f /data/reference/ucsc/hg19/hg19.fa -r chr22:42526560..42526563 -F 0.3 reads.bam 2> /dev/null| cut -f1-6 | grep -v "##"
chr22	42526561	.	GG	TC	49314.7

But I don't want MNPs, I want two SNPs. So I'll use the --no-mnps flag, right? Doesn't work:

$ freebayes -f /data/reference/ucsc/hg19/hg19.fa -r chr22:42526560..42526563 -F 0.3 --no-mnps reads.bam 2> /dev/null| cut -f1-6 | grep -v "##"
chr22	42526561	.	GGTGGTGGGGCATCCTCAGG	TCTGTAGGGGCATCCTCAGG,TCTCGGTAGGGGAGCCTCAGG,TCTGTAGGGAGCCTCAGG,TCTGGCAGGGGAGCCTCAGG,TCCGGTAGGGGAGCCTCAGG,TCTGTACGGGGAGCCTCAGG,TCAGGTAGGGGAGCCTCAGG,TCTGGGTAGGGGAGCCTCAGG,TCTAGTAGGGGAGCCTCAGG,TCTGGTTAGGGGAGCCTCAGG,TCCGGTAGGGGAGCCTTAGC,TCTGGGAGGGGAGCCTCAGG,TCTGTTAGGGGAGCCTCAGG,TCTGTAGGGAGCTCAGG,TCTTGTAGGGGAGCCTCAGG,TCTCGGTAGGGGAGCCGTCAGG,TCTCGGTACGGGGAGCCTCAGG,TTCGGTACGGGGAGCCGCTCAGG	14761.8

OK, so how about adding in --no-complex? That doesn't even give the best SNPs:

$ freebayes -f /data/reference/ucsc/hg19/hg19.fa -r chr22:42526560..42526563 -F 0.3 --no-mnps --no-complex reads.bam 2> /dev/null| cut -f1-6 | grep -v "##"
chr22	42526561	.	G	C	62.4447
chr22	42526562	.	G	C	0.0781914

Weird, so what about trying to force it to produce the best alleles?

$ freebayes -f /data/reference/ucsc/hg19/hg19.fa -r chr22:42526560..42526563 -F 0.3 --use-best-n-alleles 1 --no-mnps --no-complex reads.bam 2> /dev/null| cut -f1-6 | grep -v "##"
chr22	42526561	.	G	C	62.4447
chr22	42526562	.	G	C	0.0781914

So how I can get freebayes to report the GG/TC as two individual SNPs?