Hi, Does ‘bedtool bamtofastq’ handle supplementary reads correctly (or the version you are using)?
Regards, Keiran Raine Principal Bioinformatician Cancer Genome Project Wellcome Trust Sanger Institute [email protected] Tel:+44 (0)1223 834244 Ext: 7703 Office: H104 > On 12 Feb 2016, at 16:49, Richard Corbett <[email protected]> wrote: > > Hi Nitin, > > I think I saw this error years ago when I was working with a bam that > had multiple reads with the same name. How many times do you see > > ST1023:220:H84P1ADXX:2:2115:7649:16177 > > in your starting bam file? Are there multiple fragments (read pairs) > with the same ID? > > I think I ran in to this issue when I merged the same file multiple > times ( that was a bad day :) ) > > Richard > > > On 02/12/2016 08:43 AM, Nitin Bhardwaj wrote: >> >> Hi, >> >> I saw this error encountered by a few other users and I tried all that >> was suggested but nothing worked for me. I am still getting the error >> on Picard MarkDuplicates step: >> >> Exception in thread "main" htsjdk.samtools.SAMException: Value was put into >> PairInfoMap more than once. 1: >> GIAB:HWI-ST1023:220:H84P1ADXX:2:2115:7649:16177 >> >> Here is what I did: >> >> First sorted and converted bams to fastq as I did not have original >> fastqs: >> >> samtools sort -n NIST-hg001-7001-b-ready.bam -o >> NIST-hg001-7001-b-ready.sorted.bam >> >> bedtools bamtofastq -i NIST-hg001-7001-b-ready.sorted.bam -fq >> NIST-hg001-7001-b-ready_R1.fastq -fq2 NIST-hg001-7001-b-ready_R2.fastq >> >> Then I aligned using BWA mem: >> >> bwa mem -t 8 -M -R '@RG\tID:GIAB\tSM:NA12878\tPL:illumina\tLB:lib\tPU:7001' >> reference_genome/hg19 NIST-hg001-7001-ready_R1.fastq >> NIST-hg001-7001-ready_R2.fastq > NIST-hg001-7001.sam >> >> Sort Sam using Picard: >> >> java -jar picard-tools-1.119/SortSam.jar I=NIST-hg001-7001.sam >> O=NIST-hg001-7001_sorted.bam SO=coordinate CREATE_INDEX=true >> >> And mark duplicates: >> >> java -jar picard-tools-1.119/MarkDuplicates.jar I=NIST-hg001-7001_sorted.bam >> O=NIST-hg001-7001_dedup.bam M=NIST-hg001-7001.metric >> >> When it gives the error: >> >> Exception in thread "main" htsjdk.samtools.SAMException: Value was put into >> PairInfoMap more than once. 1: >> GIAB:HWI-ST1023:220:H84P1ADXX:2:2115:7649:16177 >> >> I tried to clean the bam using Samtools: >> >> samtools view -h NIST-hg001-7001_sorted.bam | grep -v null | samtools view >> -bS - > cleaned.bam >> >> And also used FixMateInformation using Picard: >> >> java -jar >> /home/nitin/Bioinformatics/Toolbox/src/Misc/picard-tools-1.119/FixMateInformation.jar >> I=NIST-hg001-7001_sorted.bam O=NIST-hg001-7001_fixedMate.bam >> >> But none of them worked. I still get the same error. >> >> Does anybody have a solution. I have spent a lot of time on it without >> any use. Thank a lot in advance. >> >> ~N >> >> > > -- > The contents of this electronic mail transmission are intended to be > CONFIDENTIAL and for the sole use of the designated recipient. If this > message has been misdirected, please contact the sender as soon as possible. > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=272487151&iu=/4140 > _______________________________________________ > Samtools-help mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/samtools-help
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