How to fix the BAM file (SAM validation error)

Question

[Esther Brasil]

I get the following error when I try to build the index of my BAM file:

Exception in thread "main" htsjdk.samtools.SAMFormatException: SAM validation error: ERROR: Record 3009, Read name M00918:82:000000000-BMF6N:1:1101:10112:22298, bin field of BAM record does not equal value computed based on alignment start and end, and length of sequence to which read is aligned
at htsjdk.samtools.SAMUtils.processValidationErrors(SAMUtils.java:439)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.advance(BAMFileReader.java:644)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:629)
at htsjdk.samtools.BAMFileReader$BAMFileIterator.next(BAMFileReader.java:599)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.advance(BAMFileReader.java:832)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:822)
at htsjdk.samtools.BAMFileReader$BAMQueryFilteringIterator.next(BAMFileReader.java:788)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:544)
at htsjdk.samtools.SamReader$AssertingIterator.next(SamReader.java:518)

The command is:

java -jar picard.jar BuildBamIndex I=myfile.bam

I know I can set VALIDATION_STRINGENCY=LENIENTE, but I want to fix my BAM file because it is another program that is calling it (Astrolabe, which I don't have the source).

I also could revert the Astrolabe classes to java file and try to debug and change, but if someone could suggest me an quickier solution, I would appreciate.

[Devon Ryan]

Just use samtools index instead, it likely won't complain about this.

Answer 1

[h.mon]

See SAM bin field error for the GATK run for possible solutions.

[Esther Brasil]

Thanks for the link: I will try the solution: java -cp /path/to/picard/bin/htsjdk-1.133.jar htsjdk.samtools.FixBAMFile source.bam fixed.bam (EDIT: it worked. Thank you so much! You saved me a lot of time)

Answer 2

[Pierre Lindenbaum]

another solution

• checkout picard, https://github.com/broadinstitute/picard
• change src/main/java/picard/cmdline/CommandLineProgram.java on line

https://github.com/broadinstitute/picard/blob/b2a6985ed1cdbbbb03930e40cf7b077e487aba6a/src/main/java/picard/cmdline/CommandLineProgram.java#L104

change

 public ValidationStringency VALIDATION_STRINGENCY = ValidationStringency.DEFAULT_STRINGENCY;

to

 public ValidationStringency VALIDATION_STRINGENCY = ValidationStringency.LENIENT;

recompile/re-install picard (see https://github.com/broadinstitute/picard for instruction )

---

add the following option

VALIDATION_STRINGENCY=LENIENT

see https://broadinstitute.github.io/picard/command-line-overview.html "Standard Options"

[Esther Brasil]

Dear Pierre, thanks very much for your answer, but, as I said in the question, I aware of that I can set VALIDATION_STRINGENCY=LENIENTE, but I want to fix my BAM file because it is another program that is calling it (Astrolabe, which I don't have the source).

[Pierre Lindenbaum]

ah yes, sorry, my bad, I didn't take the time to read the whole question....

[Pierre Lindenbaum]

I updated my answer.