CrossMap BAM (version 0.6.1+galaxy0)

BAM file:

Source for LiftOver Data (chain file):

Lift Over To:

Add optional BAM Headers:

Insert size:

Average insert size of pair-end sequencing (bp)

Insert size std. dev:

Stanadard deviation of insert size

Insert size std. dev foldchange:

A mapped pair is considered as 'proper pair' if both ends mapped to different strand and the distance between them is less then '-t' * stdev from the mean

CrossMap

CrossMap is versatile tool to convert genome coordinates or annotation files between genome assemblies. It supports mostly commonly used file types, including BAM, BED,BigWig, GFF, GTF, SAM, Wiggle, and VCF formats. For large plain text file types, such as BED, GFF, GTF and VCF, reading from remote servers and file compression are supported.

BAM

CrossMap updates chromosomes, genome coordinates, header sections, and all BAM flags accordingly. The program version (of CrossMap) is inserted into the header section, along with the names of the original BAM file and the chain file. For pair-end sequencing, insert size is also recalculated.

Optional tags

Q: QC. QC failed.
N: Unmapped. Originally unmapped or originally mapped but failed to liftover to new assembly.
M: Multiple mapped. Alignment can be liftover to multiple places.
U: Unique mapped. Alignment can be liftover to only 1 place.

Tags for pair-end sequencing include:

QF: QC failed
NN: both read1 and read2 unmapped
NU: read1 unmapped, read2 unique mapped
NM: read1 unmapped, multiple mapped
UN: read1 uniquely mapped, read2 unmap
UU: both read1 and read2 uniquely mapped
UM: read1 uniquely mapped, read2 multiple mapped
MN: read1 multiple mapped, read2 unmapped
MU: read1 multiple mapped, read2 unique mapped
MM: both read1 and read2 multiple mapped

Tags for single-end sequencing include

QF: QC failed
SN: unmaped
SM: multiple mapped
SU: uniquely mapped