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Old 08-26-2020, 10:58 AM   #1
Location: Fargo

Join Date: Dec 2011
Posts: 66
Default 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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