copmaring mpileup parameters: -B vs -BQ0
0
0
Entering edit mode
9.1 years ago
-_- ★ 1.1k

Hi there, I have seen the following difference which I cannot explain with samtools mpileup.

First, only -B is specified to disable BAQ calculation, it finds two reads with insertions. I am not sure if this matters, but if you look closely, the two inserted sequences are NOT exactly the same.

$ samtools mpileup -B -f ${REF} ${BAM_FILE} | grep 175200931
[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
chr1    175200931    a    20    ....,...+30CATGAATATATACACACGTATATATACATA..+30CATGTATATATACACACGTATATATACATA..........    Jm_sEHIDFsEHIdJ>JLJD

Second, I rerun the experiment with -BQ0 specified, a third insertion appears.

$ samtools mpileup -BQ0 -f ${REF} ${BAM_FILE} | grep 175200931

[mpileup] 1 samples in 1 input files
<mpileup> Set max per-file depth to 8000
chr1    175200931    a    27    ...,.,...+30CATGAATATATACACACGTATATATACATA..+30CATGTATATATACACACGTATATATACATA...,+30catgtatatatacacacgtatatatacata......,,,,..    Jm_!sEHIDFsEHI!dJ>JLJ!!!!,D

From my understanding of -Q0, it means skip bases with BAQ smaller than 0. In other words, since BAQ cannot be samller than 0, it keep all reads whatever their BAQ are.

However, I don't understand if -B is speicified to disable BAQ calculation already, why would -Q0 make a difference? Where comes the BAQ data then?

samtools mpileup BAQ • 2.0k views
ADD COMMENT

Login before adding your answer.

Traffic: 1791 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6