failed to convert from cram to bam

Question

[kygppyou]

I got a cram file, and want to convert it to bam file. Here's the command I use and error I got

samtools view -b -T human_g1k_v37.fasta lucky.cram > lucky.bam
[sam_header_read2] 84 sequences loaded.
[sam_read1] reference 'Wm�;�����e��i���f�[�=���~��Ç߼���U��/���>���Q���O����n����O��' is recognized as '*'.
Parse error at line 1: invalid CIGAR character

I don't know what to do with this. Please help~

[venu]

Convert a CRAM file to a BAM file

[Devon Ryan]

Is cram-tools even still supported?

[Devon Ryan]

This suggests that there's a mismatch between the fasta file and what the CRAM file was created with. I'd double check that before proceeding.

Answer 1

[John Marshall]

You are using a prehistoric version of samtools, one that predates the CRAM format by several years, so of course it has no support for CRAM files. (The error messages shown indicate that it is attempting to parse the input as a SAM file, and failing miserably.)

You need at least samtools 1.0 to read CRAM files, and many CRAM-related improvements were made in 1.2. Of course, what you really want to install is the most up-to-date version of samtools, which is 1.3.1 at the time of writing.