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SAM header has duplicate sorting order (SO) fields #95

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zaeleus opened this issue Apr 20, 2022 · 0 comments
Open

SAM header has duplicate sorting order (SO) fields #95

zaeleus opened this issue Apr 20, 2022 · 0 comments

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@zaeleus
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zaeleus commented Apr 20, 2022

I noticed in ENCFF659AUS that the header tag has duplicate sorting order (SO) fields.

$ samtools view --header-only https://www.encodeproject.org/files/ENCFF659AUS/@@download/ENCFF659AUS.bam | head -1
@HD	VN:1.4	SO:coordinate	SO:coordinate

While this is undefined in the specified SAM version (1.4), it should be noted that it is illegal in SAM 1.6:

Within each (non-@CO) header line, no field tag may appear more than once and the order in which the fields appear is not significant.

This issue is caused by --outSAMheaderHD including the SO field and --outSAMtype being set to SortedByCoordinate, which causes STAR to indiscriminately duplicate the field.
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