Issues With Cram -> Fastq from GTEx v8 WGS

Question

[Vullnet]

First, I wasn't sure what version of the reference genome GTEx v8 WGS generates for cram. I chose hg38.p10, and README says the human reference genome build b38 (including all decoy sequences and HLA regions). The later problem is that when samtools is used to convert cram into fastq file, a fastq file of a certain size will be generated, but samtools keeps running, running on very low CPU, and no error is reported. I don't know whether it is the problem of the reference genome version or the problem of samtools. Thank you!

samtools fastq -1 output.fq1 -2 output.fq2 -0 /dev/null -s /dev/null -n -T reference.fa input.cram

[Pierre Lindenbaum]

unless your cram in sorted on query rather than on coordinate, your cram must be first sort processed with collate:

Command line to remap a position sorted bam: "samtools collate -uOn128 old-pos-srt.bam tmpxyz | samtools fastq - | bwa mem -pt16 ref.fa - | samtools sort --threads=4 -m4G -o new-pos-srt.bam"

— Heng Li (@lh3lh3) May 26, 2019