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2021-12-03 08:48:22 -0600 | answered a question | How can I load a file in CRAM format into my GH browser? A workaround I used was to install the open-source samtools software, and convert from the CRAM to BAM format via the command: Note you can speed this up by using, say 24 threads via: This will work if your CRAM file has header information that provides MD5 sums for the reference sequence, and samtools will even automatically download needed reference data for you (into ~/.cache/hts-ref/), see this post: https://www.biostars.org/p/489646/ If you have the reference sequence FASTA file that was used to build the CRAM file, you can specify it (say it was called ref.fa) by running the command: samtools is available here: http://www.htslib.org/ Under Ubuntu I was able to install samtools (though not the latest version) via: Under RedHat / CentOS I was able to install samtools via: |