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Where to download BAM files required for PON in Mutect2 worksheets given for Workshop 1803

I am beginner and have just started using GATK. I was following the worksheets for Workshop 1803, specifically the worksheet on Mutect2 basics. There is an exercise on PONs, and it requires HG00190.bam, NA19771.bam and HG02759.bam. These are not provided with the Gatk Bundle of the workshop. When i rand the commands, I got the error "unable to read non-existent file." I read in the worksheet that these are retrieved from 1000 genomes and I was able to track down the locations of files corresponding to them, but they are all CRAM files. All of them have sizes around 3 GB, whereas the normal and tumor bam files (provided in the bundle) are only of around 250 MB size. I have the following queries -

1. Is there any link to download the BAM files directly ?
2. Should I download the CRAM files and convert them to BAM ?

The links that I have found for these are the following -

HG00190 - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/data/FIN/HG00190/exome_alignment/
NA19771 - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/data/MXL/NA19771/
HG02759 - ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/data/GWD/HG02759/

Answers

  • SheilaSheila Broad InstituteMember, Broadie admin

    @shivanisane
    Hi,

    The PoN creation step is shown for example purposes and not for running in the workshop. That is why the BAM files are not included. You can simply choose 3 BAM files you have to test the PoN creation step. If you have to run on the example BAMs we show, yes, you can convert from CRAM to BAM from the 1000Genomes ftp.

    -Sheila

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