[narain]

@lh3

Thank you for pointing out that this discussion has nothing to do with Bowtie2 vs BWA and I should address it in another thread. I noticed there is already a thread running which raises concern for using mpileup output via bcftools to get SNPs and InDels, and so I just raised my concern there itself. Here is the link: http://seqanswers.com/forums/showthr...034#post105034 . Do let me know what 'awk' command to use from the mpileup output if bcftools is not to be used. I have also sent an email to samtools-help mailing list as per your suggestion.

[abi]

@narain and @lh3

I tried exactly the same stuff as described by you for SNPs and InDels detection and landed into same conclusion that Samtools misses a lot of SNPs and InDels otherwise pointed by IGV. Here are the details of my query: http://seqanswers.com/forums/showthread.php?t=26496 . I guess the answer is simple, there got to be better tools to extract SNPs and InDels from BAM files. Have you tried GATK / Dindel ?

Abi

[sdriscoll]

this thread should be split out into a "shi vs lh3" thread.

[fei_deng]

i use bowtie2 and the result show that the uniq-map is " 24824681 (15.15%) aligned concordantly exactly 1 time",i think it is too small and i will try to use bwa.My reference is maize.