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mosdepth (Brent Pedersen, Aaron Quinlan), for depth of coverage calculations, supports threads (decompression threads with speed ups limited to 4 cpu). It is faster than CollectWgsMetrics and samtools depth and has a variety of useful options and outputs for WGS and targeted sequencing. It uses only around 1-2 GB of memory.
Comparison:
Coverage differences are likely due to different cutoffs that can be changed.
Tool
Sample
BAM size
run time
cpu
memory
mean coverage
CollectWgsMetrics
PCAWG-63_SA65868.bam
177 GB
4h 24m
54%
1.3 GB
29.4x
CollectWgsMetrics
PCAWG-63_SA65784.bam
295 GB
6h 42m
62%
1.3 GB
50.2x
mosdepth
PCAWG-63_SA65868.bam
177 GB
1h 23m
<300%
< 2 GB
34.5x
mosdepth
PCAWG-63_SA65784.bam
295 GB
2h 38m
<300%
< 2 GB
56x
It also has an option for d4 output format - "better than bigwig"
mosdepth (Brent Pedersen, Aaron Quinlan), for depth of coverage calculations, supports threads (decompression threads with speed ups limited to 4 cpu). It is faster than
CollectWgsMetrics
andsamtools depth
and has a variety of useful options and outputs for WGS and targeted sequencing. It uses only around 1-2 GB of memory.Comparison:
Coverage differences are likely due to different cutoffs that can be changed.
It also has an option for
d4
output format - "better than bigwig"CollectWgsMetrics
trace files:CollectWgsMetrics
output:mosdepth
output:Windows of 500bp seem useful for WGS data. Overall mean coverage is at the bottom of the
.summary.txt
files.The text was updated successfully, but these errors were encountered: