Hi Tommy,
I’ve looked into this with the person who generated the file. Unfortunately, we
no longer have a copy of the BAM that was compressed to create the CRAM (or an
intact CRAM). Consequently, it looks like we will have to re-align the data.
In the meantime, I’ll remove the problem file fr
Hi Rob,
Apologies - I got the wrong sample (SC_GMFUL5306366 rather than the file
mentioned, SC_GMFUL5306338). I am now able to replicate the problem.
For information, yes, it was the same file as is on the FTP site.
For the correct sample, I’m seeing this too:
[alignment]:samtools view -H
SC_G
On Wed, 8 Nov 2017, Susan Fairley wrote:
Thanks for letting me know about this.
I’ve had a (very) quick look and the samtools view -H command is working for me
with v1.2.
[alignment]:samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 1.2 (using htslib 1.2.1)
[alig
Hi All,
Thanks for letting me know about this.
I’ve had a (very) quick look and the samtools view -H command is working for me
with v1.2.
[alignment]:samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 1.2 (using htslib 1.2.1)
[alignment]:samtools view -H
SC_GMFUL5
On 8 Nov 2017, at 11:36, Tommy Carstensen
mailto:t...@sanger.ac.uk>> wrote:
2) Furthermore, when typing the command below:
samtools view -H
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/gambian_genome_variation_project/data/FULA/SC_GMFUL5306338/alignment/SC_GMFUL5306338.alt_bwamem_GRC
On Wed, 8 Nov 2017, Tommy Carstensen wrote:
To samtools-help,
1) I am trying to convert a cram to bam with samtools view v1.5, but eventually
I get the error below for some of the files, whereas others are successfully
converted:
Block CRC32 failure
[main_samview] truncated file.
Has anyone
