Why there is huge difference in mapping quality with bwa & bowtie

Question

[Govardhan Anande]

Hie NGS Geeks,

Recently I observed some huge difference in mapping quality when aligned with bowtie & bwa, after alignment I called variants using samtools mpileup. I thought someone might enlighten my knowledge about this, so my observations are

1. With bowtie I got mapping quality 2 & quality 6.98 for particular position and when I called variants using samtools surprisingly it didn't report.

Particular position in VCF file for reference:

SL2.50ch01      559045  .       G       .       6.98    .       DP=143;VDB=0.0001;AF1=1;AC1=2;DP4=0,0,64,71;MQ=2;FQ=-282        PL:DP27:135"

1. \but with bwa I got mapping quality 10 & quality 78 plus it reported variant i.e. alternate allele.

Particular position in VCF file for reference:

SL2.50ch01      559045  .       G       T       78      .       DP=58;VDB=0.0001;AF1=1;AC1=2;DP4=0,0,28,28;MQ=10;FQ=-196        GT:PL:DP:GQ   1/1:111,169,0:56:99".

I think am not confusing anyone, if so please let me know & thanks in advance

Answer 1

[lh3]

See section 3.3.2 in http://arxiv.org/pdf/1404.0929v1.pdf

[Govardhan Anande]

Thank you very much, It helped me to understand the basic since of alignment & variant calling. So ultimately which tool will you suggest for calling variants(i.e. SNPs & Indels)

[ngsgene]

There are some very interesting discussion posts that you can check, pertaining to the data/analysis you may choose one over the other at different times

Bowtie Vs Bwa For Indels

http://seqanswers.com/forums/showthread.php?t=15200

How To Compare The Performance Of Bwa And Bowtie