Truncated bam file after running ReplaceSamHeader(Picard)

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kostas alexiou

• November 17, 2020 15:12

Hi guys,

I want to modify the header of a bam file, in order to remove all the un-anchored scaffolds, and following the steps below:

1. get the modified header from the input bam file

samtools view -H input.bam | grep -v scaffold | samtools view -bh - > header.bam

2. Reheading

java -jar /opt/picard-tools-1.110/ReplaceSamHeader.jar I=input.bam HEADER=header.bam O=y.bam

3. Flagstat with samtools

samtools flagstat y.bam

[bam_flagstat_core] Truncated file? Continue anyway.
98 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
98 + 0 mapped (100.00% : N/A)
98 + 0 paired in sequencing
49 + 0 read1
49 + 0 read2
94 + 0 properly paired (95.92% : N/A)
98 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
4 + 0 with mate mapped to a different chr
4 + 0 with mate mapped to a different chr (mapQ>=5)

Flagstat of input.bam

416333 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
416333 + 0 mapped (100.00% : N/A)
416333 + 0 paired in sequencing
210024 + 0 read1
206309 + 0 read2
380475 + 0 properly paired (91.39% : N/A)
414402 + 0 with itself and mate mapped
1931 + 0 singletons (0.46% : N/A)
31200 + 0 with mate mapped to a different chr
26679 + 0 with mate mapped to a different chr (mapQ>=5)

Any help will be deeply appreciated!

Thanks

0

• 

  Genevieve Brandt

  • November 17, 2020 21:32

  Hi kostas alexiou, what is your question? One note - I would recommend updating your GATK version, you are using a very old version of PICARD. 

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  kostas alexiou

  • November 18, 2020 07:53
  • Edited

  Hi Genevieve Brandt. Sorry. I was not very clear in my message. My question was why I am getting a truncated bam file, after running the ReplaceSamHeader tool from picard. As you have suggested, I have run picard with the latest release (v2.23.8) but still getting a truncated bam file. Below is the command that I am using and the flagstat of the output and input files.

  java -jar ~/local/software/picard.jar ReplaceSamHeader -I Olea01_genes.bam -HEADER header.bam -O x.bam

  $ samtools flagstat x.bam
  [bam_flagstat_core] Truncated file? Continue anyway.
  155 + 0 in total (QC-passed reads + QC-failed reads)
  0 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  155 + 0 mapped (100.00% : N/A)
  155 + 0 paired in sequencing
  76 + 0 read1
  79 + 0 read2
  149 + 0 properly paired (96.13% : N/A)
  155 + 0 with itself and mate mapped
  0 + 0 singletons (0.00% : N/A)
  4 + 0 with mate mapped to a different chr
  4 + 0 with mate mapped to a different chr (mapQ>=5)

  $ samtools flagstat Olea01_genes.bam
  484958 + 0 in total (QC-passed reads + QC-failed reads)
  0 + 0 secondary
  0 + 0 supplementary
  0 + 0 duplicates
  484958 + 0 mapped (100.00% : N/A)
  484958 + 0 paired in sequencing
  243866 + 0 read1
  241092 + 0 read2
  447722 + 0 properly paired (92.32% : N/A)
  482402 + 0 with itself and mate mapped
  2556 + 0 singletons (0.53% : N/A)
  31940 + 0 with mate mapped to a different chr
  27693 + 0 with mate mapped to a different chr (mapQ>=5)

   

  Thanks!

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  kostas alexiou

  • November 18, 2020 23:33

  I have managed to solve the problem of the truncated file. After all, the reheading was not working because there were reads whose mate was mapping to a different chromosome/scaffold and that this wasn't present in the new header.

  Best

  Kostas

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  Genevieve Brandt

  • November 19, 2020 16:48

  Hi kostas alexiou, thank you for the update, glad you were able to solve the problem!

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