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What is the difference between -BadMateFilter and -MappingQualityFilter in Unifiedgenotyper?

Posts: 23Member
edited October 2012

It was a bit unclear what the BadMateFilter is doing in the documentation. Any information would be appreciated!

Post edited by Geraldine_VdAuwera on
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Answers

• Posts: 35Member

To follow up with this question: What information from the bam file does this filter need?

• Posts: 8,171Administrator, GATK Dev admin

@Sophia said:
To follow up with this question: What information from the bam file does this filter need?

Which one? Bad Mate or MappingQuality?

Geraldine Van der Auwera, PhD

• Posts: 35Member
edited October 2013

@Geraldine_VdAuwera said:
Which one? Bad Mate or MappingQuality?

The BadMateFilter.

Post edited by Sophia on
• Posts: 8,171Administrator, GATK Dev admin

BadMateFilter will look at the SAM flags for read paired (1), unmapped read (4), and will check whether the read and its mate are indexed on the same contig.

Geraldine Van der Auwera, PhD

• AustraliaPosts: 1Member

Hello there, I have reads from GBS experiments where in the library production process many reads concatemerised. The consequence is that about 40% of the reads get filtered by the 'BadMateFilter' and I have to be able to switch it off. How? any help is greatly appreciated.
cheers
Norman

• Posts: 8,171Administrator, GATK Dev admin

Hi @norman,

It's not possible to switch off the filters, so you'll need to fix your bam file so that read mate status is correct. I'm not sure how to do that though, and it's not a GATK-specific issue, so I would recommend asking in a more general forum like SeqAnswers or BioStars. Good luck!

Geraldine Van der Auwera, PhD

• Posts: 28Member

Hi,

concerning the BadMateFilter; does it remove both reads when filtering with the BadMateFilter or just one of them ?

Thanks !

• Posts: 8,171Administrator, GATK Dev admin

@Max, I believe it acts on individual reads, not pairs.

Geraldine Van der Auwera, PhD

• Posts: 483Member, GATK Dev, DSDE Dev mod

@Geraldine_VdAuwera‌, can you clarify that? I don't doubt that the filter works on individual reads, but my read of @Max's question is that he's asking whether it will kick out the whole pair or choose one of the reads to keep. It doesn't make sense to me that it would keep one of the reads, and I don't see anything in the code to indicate that either. I think it will filter out both reads, as they both fail to satisfy the question "Is this read's chromosome the same as it's mate's chromosome?"

• Posts: 8,171Administrator, GATK Dev admin

I fully expect that both reads in a pair would fail the filter, so the end result would be that the entire pair would be filtered, yes. But to be clear, the read filter doesn't have visibility on the mate when it does the filtering.

Geraldine Van der Auwera, PhD

• Posts: 28Member

Ah okay, that makes sense. Thanks for the answers !

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