Hi All,
I test samtools 1.2 with and without option --skip-indels on a sample
which has an one base deletion in position 360. And they generate the SAME
mpileup results which are NOT what I expected:
$samtools/current/samtools mpileup -A --min-MQ 5 --min-BQ 30 -d 800000 -f
IST03663_S4_L001.fa IST03663_S4.bwa.mem.bam.sort.bam
-o IST03663_S4_consensus_pileup_w_indels.txt
$samtools/current/samtools mpileup --skip-indels -A --min-MQ 5 --min-BQ 30
-d 800000 -f IST03663_S4_L001.fa IST03663_S4.bwa.mem.
bam.sort.bam -o IST03663_S4_consensus_pileup_wo_indels.txt
$ diff IST03663_S4_consensus_pileup_wo_indels.txt
IST03663_S4_consensus_pileup_w_indels.txt
$ (no difference between with option �Cskip-indels and without option
�Cskip-indels).
Thanks,
Qicheng
From: Ma, Qicheng
Sent: Tuesday, September 01, 2015 10:37 AM
To: [email protected]
Subject: how to generate mpileup output for indels similar to pileup output for
indels
Hi ,
Could anyone help me how to generate mpileup output for indels similar to
old pileup output for indels ?
Here is the example, there is single base deletion at position 360.
In the old pileup output attached here, there is one more line:
WT 359 * -a/-a 23789 303081 59 7917 -a * 7505
412 0 0 0
which the new mpileup output attached here does not have.
The old pileup was generated by:
$samtools/samtools-0.1.8/samtools pileup -cf IST03663_S4_L001.fa
IST03663_S4.bwa.mem.bam.sort.bam >
IST03663_S4_consensus_pileup_w_indels_0.1.8.txt
The new mpileup was generated by:
$samtools/current/samtools mpileup -A --min-MQ 5 --min-BQ 30 -d 800000 -f
IST03663_S4_L001.fa IST03663_S4.bwa.mem.bam.sort.bam
-o IST03663_S4_consensus_pileup_w_indels.txt
Thanks,
Best regards, Mit freundlichen Grüssen, Meilleures
salutations, 此致 敬礼
Qicheng Ma<http://publicationslist.org/qicheng.ma>, Ph. D.
Investigator III
Novartis Institutes for BioMedical
Research, Inc.
220 Massachusetts Avenue
Cambridge, MA 02139
USA
Phone +1 617 8717218
Fax +1 617 8715783
[email protected]<mailto:[email protected]>
http://www.nibr.com/research/discovery/pathways.shtml
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