This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
Gathered bam could not be indexed
I runed indelRealigner of the same bam for 32 times each with a -L option which specify an interval, then I gathered the bam files of the outputs using picard GatherBamFiles(I found that the gather function of bam gather is a wrapper of picard GatherBamFiles). Then I have a large bam file, but when I tried to index the bam file, there is this error:
[E::bgzf_read] bgzf_read_block error -1 after 147 of 254 bytes
samtools index: "gathered.bam" is corrupted or unsorted
I dont know why is this, could anyone help me? thanks a lot.