To whom it may concern,
I met a problem when using samtools-1.0 mpileup to deal with a pairend reads
mapping result file in sort bam format. The command I used was:
samtools mpileup -B -Q 0 -d 999999999 -f ref_all_C-T_G-A.fa mapping_ms.sort.bam
> mapping_ms.sort.bam.pile
Following are two paired reads from file "mapping_ms.sort.bam":
seq.5547# 97 chr10_C-T 292795 255 100M = 294319
1624
GTGATGAGTTGGAGTTGTATTAGTGTTTTTTATGAGAAGGGAGATTTTGGAAATTTAAGAATGATGATTGAGGTGAGGAAGAGGTAGAATTGAGTATTTT
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:64G26T8
YS:i:0 YT:Z:DP NH:i:1
seq.5547# 145 chr10_C-T 294319 255 100M = 292795
-1624
TATTTATGATGTTTTAGTTTATTGAAAAAGTTTTTGTGTTAATTTAGATAAAGAAGTTAAGTGTTTTTTTATTAAGAATGTTGTATTGGAGTATTTAGAT
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YS:i:-12
YT:Z:DP NH:i:1
seq.346110# 99 chr10_C-T 294276 255 100M = 294316
140
GAATTAGAGTTTGAAATAGAAGTAGTAAGTTTTAGTTAGGAAATATTTATGATGTTTTAGTTTATTGAAAAAGTTTTTGTGTTAATTTAGATAAAGAAGT
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YS:i:0 YT:Z:CP
NH:i:1
seq.346110# 147 chr10_C-T 294316 255 100M = 294276
-140
AAATATTTATGATGTTTTAGTTTATTGAAAAAGTTTTTGTGTTAATTTAGATAAAGAAGTTAAGTGTTTTTTTATTAAGAATGTTGTATTGGAGTATTTA
gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100 YS:i:0 YT:Z:CP
NH:i:1
This is one line from the result file "mapping_ms.sort.bam.pile":
chr10_C-T 294382 T 1 , g
From the bam file we could easily know that for position "294382" the depth
should be 2 insead of 1. What options should I use if I don't want to filter
any reads when generated the result file?
Thanks very much for your time and I am looking forward to your reply.
Fang Liang
Beijing Institute of Genomics, Chinese Academy of Science
-----原始邮件-----
发件人: "Heng Li" <[email protected]>
发送时间: 2015-08-18 23:07:24 (星期二)
收件人: "梁芳" <[email protected]>
抄送: "李茹姣" <[email protected]>
主题: Re: regarding to the result samtools mpileup
The first read is unpaired. mpileup doesn't use it by default. Please ask
[email protected] if you have further questions.
Heng
On Aug 18, 2015, at 5:14 AM, 梁芳 <[email protected]> wrote:
> Dear Dr Li,
>
> I met a problem when using samtools-1.0 mpileup to deal with a mapping result
> file in sort bam format. The command I used is:
>
> Following is the command I used to generate the mpileup file:
> samtools mpileup -B -Q 0 -d 999999999 -f ref_all_C-T_G-A.fa
> mapping_ms.sort.bam > mapping_ms.sort.bam.pile
>
>
> This is part of the result file:
>
> chr10_C-T 288153 A 1 . g
> chr10_C-T 288154 T 1 . g
> chr10_C-T 288155 T 1 . g
> chr10_C-T 288156 A 1 . g
> chr10_C-T 288157 G 1 . g
>
>
> Here are two reads from the file mapping_ms.sort.bam from which we could see
> the depth should be 2 for the above position "288155" instead of depth 1.
>
> seq.197749# 153 2 chr10_C-T 288137 255 100M =
> 288137 0
> GTTTGATGATTTTTTTATTAGAGATGTATGAAGTTTATTTTAAATTGGAAAAAAAAAATATATTATGTATTTAAGAATATGTTTTAAGATAAATTGTTTT
>
> gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
> AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:100YT:Z:UP NH:i:1
> seq.11071# 99 1 chr10_C-T 288146 255 100M =
> 288392 346
> TTTTTTTATTAGAGATGTATGAAGTTTATTTTAAATTGGAAAAAAAAAATATAGTATGTATTTAAGAATATGTTTTAAGATAAATTGTTTTTAGATATTT
>
> gggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggggg
> AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:53T46 YS:i:-12
> YT:Z:CP NH:i:1
>
>
> What options should I use if I don't want to filter any reads when generated
> the result file?
>
>
> Thanks for your consideration!
>
> 李博士，您好，我是想请教您如何才能让mpileup的输出结果里含有输入文件所有reads的覆盖度信息，就是不想过滤掉任何一条read.
>
>
> Fang Liang
> Beijing Institute of Genomics, Chinese Academy of Science
>
>
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