Hi,
I'm doing some experiments with cram files, I'm working with high coverage
.bam file from
ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/phase3/data/NA12878/high_coverage_alignment
First I extract only chromosome 20 and then I try to convert it to cram
format, the commands I run are:
samtools view -h -b
NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906.bam -o
high20.bam 20
samtools view -C -T human_g1k_v37.fasta -o chrom_20.cram high20.bam
And I get the next error:
Failed to populate reference for id 84
[main_samview] failed to write the SAM header
Nevertheless, if I run exactly the same commands with the low coverage
file, I don't get any error.
I'm using last version of samtools 1.3.1. Do you have any idea what's the
error about it?
I'll really appreciate your help!
Thanks,
Veronica
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