I am using samtools to call variants in a haploid genome (yes I know it is designed for diploid). It finds SNPs easily, and most of the indels, but there are a few indels it can NOT seem to find no matter what parameters I give it. I use bwa mem for the alignment of MiSeq PE 150 reads, and I get about 150x coverage, all good. Using tview etc, there is clearly a G deletion at position 600, but bcftools will not seem to call it, despite calling some nearby (~100bp before). All the mapping and base qualities seem to be fine.
This is the command I am using:
samtools mpileup -B -g -u -f ref.fa aln.bam | bcftools view -v -
It happens whether I use the -B or not.
Any help appreciated.
Below is the INDEL position pileup +/- 2 bases:
Contig_Plasmid 598 C 185 ....,,,..,,,.,,,,,,..........,...,.,,,....,,.$,$,.,....,.,,...,,......,,,...,,,,,,,,,,,,,,....,...,,,.,.....,.,,.,....................,,,,,,,,.....,.,.,..,,,,,,
,,,,,,,.,,.....,,,,,,..,.., BHHHCBFHHGGGHGGGGGGHHGHHGDHHHGHHHGHHHHFHHHHHHAHHHHHHGGGHHFHHIGHFHHHHHHHHHHHHGHHHHHHHHHEHD5FH2HH?GHHHGIHHIHHHFHHGGHHHBHHHHGGHHHHHHHHHFHHHHGHHFGHHHHHHHHHHHGHGHHHHHHH?HHBH
FFFFFHHHHHHB@HCDH
Contig_Plasmid 599 A 183 ....,$,$,..,,,.,,,,,,..........,...,.,,,....,,,.,....,.,,...,,......,,,...,,,,,,,,,,,,,,....,...,,,.,.....,.,,.,....................,,,,,,,,.....,.,.,..,,,,,,,,
,,,,,., ...