Can I Use The Gatk Snp Calling On Sam Files With Missing Quality Values

Question

[Varun Gupta]

Hello Everyone

I have a set of bam files obtained by using bowtie1 as aligner. I want to use GATK's current version for carrying out snp calling.

When I run GATK's current version of snp calling, I get this error

MappingQualityUnavailableFilter

Looking more carefully at the bam files, I noticed that 5th column has 255 as quality score which means mapping quality unavailable.

Going through blogs I came across this post where reverting back to a previous version of GATK fixed the issue

http://seqanswers.com/forums/archive/index.php/t-15086.html

Now bowtie always produce quality score of 255.

I am interested in using current GATK version for snp calling. The version used above in the post is very very old. Is there a way i can modify the existing bam files obtained from bowtie so that i can use it with current GATK version of snp calling.

PS: Ofcourse i can map the reads with bwa

Hope to hear from you soon

Regards

Varun

Answer 1

[Istvan Albert]

This is a limitation of the mapper, it was not built to fill in the quality field.

You can't meaningfully fix that value without actually realigning the reads with a different aligner.

You might try to replace this with another fixed but valid value.

[Varun Gupta]

Hi Istvan

So should I try mapping my reads with bwa and then use GATK current version for snp calling??

[Istvan Albert]

that is now a different question to which the correct answer will depend on many factors - mainly if it feasible and desirable to rerun the mapping.

Answer 2

[Ashutosh Pandey]

I think that is a pretty usual problem with people using GATK. BWA is best for alignment if you want to use GATK for SNP calling. But even if you use aligners like SHRIMP2, BOWTIE2 you can use the following trick http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_filters_ReassignOneMappingQualityFilter.html.

[Varun Gupta]

Sounds interesting

Will give it a try and tell you about it

Thanks

[Ashutosh Pandey]

Just to let you know that the fix doesn't do anything other than lowering down the MQ value of 255 value to 60 which is kind of close to a mapping score of unique alignment by BWA.

[Varun Gupta]

My main purpose is to run the current version of GATK. If that happens with this everything else is fine..

Thanks