Question: Bam-readcounts min-base-quality not giving expected output
0
gravatar for sheenams
25 days ago by
sheenams50
United States
sheenams50 wrote:

I would like to limit the base-quality-score to phred 13 (similar to default of samtools mpileup (1.3.1)), using bam-readcount (0.8.0). Despite various command modifications, I'm not getting the expected output.

Default:

bam-readcount -f human_g1k_v37.hotspot.fasta final.bam -l F5DNA.txt --max-warnings 0

1       169519049       C       8085    =:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  A:21:60.00:20.05:0.00:15:6:0.20:0.01:33.00:15:0.85:124.00:0.62  C:39:60.00:17.72:1.54:24:15:0.18:0.01:21.10:24:0.85:123.92:0.54 G:8:60.00:11.38:0.00:1:7:0.07:0.02:37.50:1:0.85:124.00:0.13     T:8014:60.00:26.69:0.04:4033:3981:0.15:0.01:35.90:4033:0.85:123.97:0.44 N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  -C:3:60.00:0.00:0.00:2:1:0.18:0.01:9.33:2:0.86:124.00:0.58

min-base-quality 13:

bam-readcount -f human_g1k_v37.hotspot.fasta final.bam -l F5DNA.txt --min-base-quality 13 --max-warnings 0

1       169519049       C       8067    =:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  A:21:60.00:20.05:0.00:15:6:0.20:0.01:33.00:15:0.85:124.00:0.62  C:27:60.00:20.70:2.22:14:13:0.16:0.01:21.04:14:0.85:123.96:0.45 G:2:60.00:24.50:0.00:1:1:0.15:0.01:24.50:1:0.85:124.00:0.44     T:8014:60.00:26.69:0.04:4033:3981:0.15:0.01:35.90:4033:0.85:123.97:0.44 N:0:0.00:0.00:0.00:0:0:0.00:0.00:0.00:0:0.00:0.00:0.00  -C:3:60.00:0.00:0.00:2:1:0.18:0.01:9.33:2:0.86:124.00:0.58

Mpileup: (-Q0, not showing the variants)

 samtools mpileup -f human_g1k_v37.hotspot.fasta -d 1000000 -A -l F5DNA.txt -Q0 final.bam 
1       169519049       C       8085

Mpileup: (default of -Q13, not showing the variants

samtools mpileup -f human_g1k_v37.hotspot.fasta -d 1000000 -A -l F5DNA.txt -Q13 final.bam 
1       169519049       C       4072

Looking at IGV, the readcounts at this position are 8085, which matches both mpileup and bam-readcount output when minimum base quality is 0. Any idea why bam-readcounts does not appear to filter the same when the minimum base quality is set to 13?

mpileup bam-readcount • 123 views
ADD COMMENTlink modified 22 days ago by Chris Miller17k • written 25 days ago by sheenams50
0
gravatar for Chris Miller
22 days ago by
Chris Miller17k
Washington University in St. Louis, MO
Chris Miller17k wrote:

answered here: https://github.com/genome/bam-readcount/issues/37

ADD COMMENTlink written 22 days ago by Chris Miller17k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 477 users visited in the last hour