Re: [Samtools-help] Cram conversion error: [main_samview] failed to write the SAM header

[Shane McCarthy]

NA12878.mapped.ILLUMINA.bwa.CEU.high_coverage_pcr_free.20130906.bam was mapped 
to the hs37d5.fa reference genome, which contains contigs not in 
human_g1k_v37.fasta. Try:

samtools view -C -T hs37d5.fa -o chrom_20.cram high20.bam


> On 26 Oct 2016, at 15:11, Veronica Suaste Morales  wrote:
> 
> 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
> --
> The Command Line: Reinvented for Modern Developers
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[Samtools-help] Cram conversion error: [main_samview] failed to write the SAM header

[Veronica Suaste Morales]

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
--
The Command Line: Reinvented for Modern Developers
Did the resurgence of CLI tooling catch you by surprise?
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Learn the new .NET and ASP.NET CLI. Get your free copy!
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Samtools-help mailing list
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