Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

ASEReadCounter does not return the value only for chrX



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    Megan Shand

    I'm not sure why chrX would be excluded, but I think fixing the sequencing dictionaries to match is the first step. If the tool runs to completion without an error and you're still not getting output for chrX then we can take a look at that issue. 

    If the only mismatches in your sequence dictionaries between the two references (the one used for the bam and the one used for the vcf) are not ones you care about (ie not autosome or chrX) then you might be able to get away with just editing the sequence dictionary in the header. Otherwise if there are differences in the main part of the genome, then you should be sure you're lifting over your VCF to the exact same reference that your BAM is aligned to.

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    Kei Enomoto

    Explicitly specifying chrX in -L argument solved the problem. I still wonder why only chrX is excluded otherwise though.

    Thank you for your help anyway!

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