Hi there,
I have a BAM file generated with strobealign 0.16.1 that includes secondary alignments; SEQ and QUAL fields are
present for primary alignments, but absent for secondary alignments.
The BAM file is filtered with samtools 1.21 using a BED file, i.e. samtools view -L interesting_genes.bed. If
the primary alignment of a read is outside of the regions defined in the BED file, but secondary alignments
lie within these regions, the filtered BAM file will only contain the secondary alignments, and none of these
will have SEQ or QUAL fields.
I'm aware that SEQ/QUAL are optional for secondary alignments, but in this case, working with the resulting
filtered BAM file becomes a little bit difficult (e.g., IGV showing only question marks).
-
Would it make sense to include SEQ/QUAL in secondary alignments during filtering when the primary alignment is filtered out?
-
Should one of the secondary alignments be promoted to primary if the original primary alignment is filtered out?
Hi there,
I have a BAM file generated with strobealign 0.16.1 that includes secondary alignments; SEQ and QUAL fields are
present for primary alignments, but absent for secondary alignments.
The BAM file is filtered with samtools 1.21 using a BED file, i.e.
samtools view -L interesting_genes.bed. Ifthe primary alignment of a read is outside of the regions defined in the BED file, but secondary alignments
lie within these regions, the filtered BAM file will only contain the secondary alignments, and none of these
will have SEQ or QUAL fields.
I'm aware that SEQ/QUAL are optional for secondary alignments, but in this case, working with the resulting
filtered BAM file becomes a little bit difficult (e.g., IGV showing only question marks).
Would it make sense to include SEQ/QUAL in secondary alignments during filtering when the primary alignment is filtered out?
Should one of the secondary alignments be promoted to primary if the original primary alignment is filtered out?