Creating Mappability Maps

[Yash Prasad]

Hi Tobias

I am having an issue while creating mappability map.

I am trying to create it for WGS and the reference fasta is "Homo_sapiens.GRCh38.dna.chromosome.all.fasta" (3.1 GB) from "this link"

Initial steps of using dicey to chop the ref fasta and indexing worked fine.

But the step of bwa aligning and then samtools sorting :-

"bwa mem -t 8 Homo_sapiens.GRCh38.dna.chromosome.all.fasta read1.fq.gz read2.fq.gz | samtools sort -@ 8 -o srt.bam -"

is unreasonably too time consuming.

We have a PBS clustering environment and I am creating a job for 165 hours (max limit) to perform this step but still it is not completing.

Do you have an idea how can I proceed in order to get the coverage information and also perform CNV analysis for WGS sample.

Thanks for the help.

Regards

Yash

[Tobias Rausch]

Hi,

Pre-built human mappability maps can be downloaded here: https://gear-genomics.embl.de/data/delly/

Best, Tobias

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[Yash Prasad]

Thanks for pointing out the location