OK, thanks again!
> -----原始邮件----- > 发件人: "Thomas W. Blackwell" <[email protected]> > 发送时间: 2015-08-26 20:59:16 (星期三) > 收件人: "梁芳" <[email protected]> > 抄送: [email protected], "李茹姣" <[email protected]> > 主题: Re: Re: [Samtools-help] Fw: Re: regarding to the result samtools mpileup > > > This doesn't seem to be implemented within mpileup. One could either > re-write > those lines using a perl or awk script, or else disable split-read alignments > during the preceding read mapping. > > - tom blackwell - > > On Wed, 26 Aug 2015, ��˧ wrote: > > > 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 > >>> > >>> > > ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
