Truncated bam file after running ReplaceSamHeader(Picard)
Answered
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
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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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Hi Genevieve Brandt (she/her). 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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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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Hi kostas alexiou, thank you for the update, glad you were able to solve the problem!
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Hi Kostas, how did you solve the issue? I seem to have the same problem
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HI elhadi iich,
Could you clarify the specific problem you are seeing and provide your output? It appears that the previous user was running into an issue when running ReplaceSamHeader because some reads in the bam file had a mate-pair mapping to a different chromosome that was not present in the new header. Could you check if this is the case for your bam file and ensure that this is accounted for in your new header?
Kind regards,
Pamela
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