There could be a mistake in bcftools/mpileup_bench/get_data.sh

[zengxiaofei]

Dear developers,

Thank you for providing such a useful tool!

I think there could be a mistake in bcftools/mpileup_bench/get_data.sh

echo "Getting PacBio $reg"
samtools view -o pacbio_50x.bam --write-index -@8 https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/ChineseTrio/HG005_NA24631_son/NIST_BGIseq_2x150bp_100x/GRCh38/HG005_GRCh38_BGIseq-2x150-100x_NIST_20211126.bam $reg

echo "Getting BGI $reg"
samtools view -o bgi_100x.bam --write-index -@8 https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/ChineseTrio/HG005_NA24631_son/PacBio_CCS_15kb_20kb_chemistry2/GRCh38/GIAB_5mC_CpG/HG005.GRCh38.deepvariant.haplotagged.bam $reg

According to the URLs, the output file name for the first command should be bgi_100x.bam, while the output file name for the second comamnd should be pacbio_50x.bam.

I'm not sure whether this will have any impact on the conclusions and parameters on -X bgi (#2045 (comment)).

Best regards,
Xiaofei

[zengxiaofei]

Close this issue as there has been no response for two months.

[pd3]

Was this closed purely for the reason of not being commented on? If the problem persists, please leave this open. It just means we are very busy.

@jkbonfield is this something that needs to be addressed?

[jkbonfield]

It looks like a typo. I obviously wasn't routinely rerunning the script to get that data as I'd already downloaded it (and it took ages). I'll fix.

[zengxiaofei]

Thanks for your reply!