While I can access the cram file using samtools view, samtools idxstats doesn't work on cram files. It ran but reported 0 for all stats apart from chromosome/contig length (a few lines below). This must be some problem of samtools accessing cram's reference registry.
>samtools idxstats >ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/hgsv_sv_discovery/data/HG00732/high_cov_alignment/HG00732.alt_bwamem_GRCh38DH.20150715.PUR.high_coverage.cram > | less chr1 248956422 0 0 chr2 242193529 0 0 chr3 198295559 0 0 chr4 190214555 0 0 chr5 181538259 0 0 chr6 170805979 0 0 Has anyone run into this issue before? Best. Holly ------------------------------------------------------------------------------ _______________________________________________ Samtools-help mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/samtools-help
