SNP and INDEL callers for novoalign or SAM?

[Nix]

Hello Folks,

I was wondering what people are using to call SNPs and INDELS from novoalign alignments? I've been converting to maq and using that package but was wondering if anything else is available.

Since novoalignments can be converted to SAM I suppose any SNP and INDEL caller that supports SAM will work. So a second question is what variant callers are out there that work with SAM alignments?

-cheers, D

[drio]

samtools and broad's gatk.

[krobison]

You'll find a bunch more in the software wiki under SNP Discovery and InDel discovery-- just look for those which have SAM or BAM as input format.

[Lee Sam]

For indel and SV analysis a large number of tools are becoming available. However, certain tools are optimized for certain SV sizes (e.g. samtools for indels > ~20bp, breakdancer for SVs > 100bp). I think Heng Li (lh3, right?) said that dindel was really good according to some early 1000genomes data.

[oiiio]

dindel, samtools, and gatk are probably your best bets. Not to mention it will probably be much easier finding support for these tools.