how to call snps with samtools from 454.bam

[krawitz]

Hi there,

I really like samtools for variant calling on Illumina.bam. However, now I have a GS Junior 454 data set. I aligned the reads via bwa bwasw and got a .sam alignment. I converted to .bam via samtools and inspected the alignment in igv. There clearly is a heterozygous SNV at (my positive control):

chr17 29556283:G>T

This position is covered by 859 reads, 52% showing the reference base G and 47% the alternating T.
I tried every modification/parameter tuning in samtools mpileup I can think of. BUT I CANNOT GET THIS VARIANT.
If anyone would like to try please write me a line and I will send the .bam file (MID1.bam 515K, MID1.bam.bai 1.3M)

I would really appreciate your help!

peter

p.s: sent email to [email protected] with subject e.g. snp calling on 454.bam

[nilshomer]

Try posting to the samtools help mailing list ([email protected]).

[ulz_peter]

Hi Peter,

I just gave it a quick shot and looked it up on UCSC GB (assuming you are working with hg19/GRCh37 build). Seems that there are some segmental duplications. This could lead to alignment on multiple sites and possibly samtools discards these sites (I don't know for sure...).