Question: Why there is huge difference in mapping quality with bwa & bowtie
gravatar for Govardhan Anande
4.8 years ago by
Govardhan Anande130 wrote:

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"

2. 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

ADD COMMENTlink modified 17 months ago by Biostar ♦♦ 20 • written 4.8 years ago by Govardhan Anande130
gravatar for lh3
4.8 years ago by
United States
lh331k wrote:

See section 3.3.2 in

ADD COMMENTlink written 4.8 years ago by lh331k

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)

ADD REPLYlink modified 4.8 years ago • written 4.8 years ago by Govardhan Anande130

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

How To Compare The Performance Of Bwa And Bowtie

ADD REPLYlink written 4.8 years ago by ngsgene350
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