CRAM to BAM using SAMTOOLS

0

Hi, I'm trying to convert a .cram file into a .bam file and then index it using the commands samtools view, samtools sort, and samtools index, but I keep getting these errors:

[W::sanitise_SQ_lines] Header @SQ length mismatch for ref chr1, 248956422 vs 1829166
[W::cram_decode_slice] Slice ends beyond reference end
[E::cram_decode_slice] MD5 checksum reference mismatch for ref 0 pos 1738847..1829166
[E::cram_decode_slice] CRAM: 7967333fff01950056c4d027080b6d64
[E::cram_decode_slice] Ref : 054a9124890edd7a99adc46514649a52
[E::cram_next_slice] Failure to decode slice
[main_samview] truncated file.

I'm pretty sure that the reference file I'm using is correct so I don't know what the problem is.

Thanks.


SAMTOOLS


CRAM


BAM

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