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  • horvathdp
    Member
    • Dec 2011
    • 66

    #1

    samtools view: failed to add PG line to the header

    So I get a error when trying to convert my sam to a bam:

    samtools view: failed to add PG line to the header

    My header seems OK (see below), but I am new at this. How do I fix my headers so my command generates a bam file

    samtools view -bS joelle.sam > joelle.bam

    @SQ SN:utg000001l LN:5073047
    @SQ SN:utg000002l LN:24568116
    @SQ SN:utg000003l LN:22903238
    @SQ SN:utg000004l LN:14007477
    @SQ SN:utg000005l LN:8330460
    @SQ SN:utg000006l LN:20648589

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