Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup

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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" <tb...@um...>
> 发送时间: 2015-08-20 21:25:48 (星期四)
> 收件人: "梁芳" <li...@bi...>
> 抄送: sam...@li..., "李茹姣" <li...@bi...>
> 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
> 
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> -----鍘熷閭欢-----
> 鍙戜欢浜� "Heng Li" <he...@br...>
> 鍙戦�佹椂闂� 2015-08-18 23:07:24 (鏄熸湡浜�)
> 鏀朵欢浜� "姊佽姵" <li...@bi...>
> 鎶勯�� "鏉庤尮濮�" <li...@bi...>
> 涓婚: Re: regarding to the result samtools mpileup
> 
> 
> The first read is unpaired. mpileup doesn't use it by default. Please ask sam...@li... if you have further questions.
> 
> 
> Heng
> 
> 
> On Aug 18, 2015, at 5:14 AM, 姊佽姵 <li...@bi...> 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
> > 
> >