How to Fix the follow ValidateSamFile error ?

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Luis Enrique Romero Cruz

• March 06, 2021 03:51

Since I had problems with some BAM files, I ran ValidateSamFile to checked them and I got the Follow error:

ERROR::INVALID_UNALIGNED_MATE_START:Record 7208324, Read name ST-E00318:811:H2YNGCCX2:2:2204:25296:14195, The unaligned mate start position is 154003504, should be 0

However, I understand what the problem is, but I can't find how to fix it.

Any suggestion?

P.D. I have tried CleanSam and FixMateInformation but it hasn't worked for me

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  Genevieve Brandt (she/her)

  • March 10, 2021 04:38

  Hi Luis Enrique Romero Cruz,

  It depends on what the cause of the issue is, you can go back to previous steps of your pipeline and determine when the issue came up and fix it there. It looks like this error message is an unaligned mate, so possibly there were issues with your alignment step.

  Best,

  Genevieve

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