Hi, Tom,
Sorry to bother you again. I have another question.
Following is one line from the result file of "samtools mpileup". Is there an
option that could filter the "reference skip" ('<' or '>') in the depth column?
chr10_C-T 3147419 G 7 <<,><>, ggggggg
For example, this is what I want:
chr10_C-T 3147419 G 2 ,, gg
Thanks!
> -----原始邮件-----
> 发件人: "Thomas W. Blackwell" <[email protected]>
> 发送时间: 2015-08-20 21:25:48 (星期四)
> 收件人: "梁芳" <[email protected]>
> 抄送: [email protected], "李茹姣" <[email protected]>
> 主题: Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup
>
>
> Might experiment with adding -A. I observe that one read pair has the
> proper pair flag set (99,147) and the other pair has it unset (97,145).
> The description for -A in the samtools 1.1 man page reads "Do not skip
> anomalous read pairs in variant calling."
>
> - tom blackwell -
>
> On Thu, 20 Aug 2015, 温帅 wrote:
>
> > 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
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> -----鍘熷閭欢-----
> 鍙戜欢浜� "Heng Li" <[email protected]>
> 鍙戦�佹椂闂� 2015-08-18 23:07:24 (鏄熸湡浜�)
> 鏀朵欢浜� "姊佽姵" <[email protected]>
> 鎶勯�� "鏉庤尮濮�" <[email protected]>
> 涓婚: 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, 姊佽姵 <[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!
> >
> > 鏉庡崥澹紝鎮ㄥソ锛屾垜鏄兂璇锋暀鎮ㄥ浣曟墠鑳借mpileup鐨勮緭鍑虹粨鏋滈噷鍚湁杈撳叆鏂囦欢鎵�鏈塺eads鐨勮鐩栧害淇℃伅锛屽氨鏄笉鎯宠繃婊ゆ帀浠讳綍涓�鏉ead.
> >
> >
> > Fang Liang
> > Beijing Institute of Genomics, Chinese Academy of Science
> >
> >
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