Stats to include in final report - Githubissues

FrickTobias / BLR

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Stats to include in final report #217

Closed pontushojer closed 3 years ago

pontushojer commented 4 years ago

These are some things that should be included in the final report, inspired by the longranger final report (example report, this page is also of interest https://support.10xgenomics.com/genome-exome/software/pipelines/latest/output/metrics):

[x] Nr of SNPs phased (percentage)
[x] Longest phase plock
[x] Nr of barcode partitions in final set
[x] N50 linked-reads per molecule (also called LPM)
[x] N50 phaseblock
[x] Mean molecule length
[x] DNA in molecules >20 kbp (percentage)
[x] DNA in molecules >100 kbp (percentage)
[x] Nr of Large structural variants
[x] Number of reads
[x] Median insert size
[x] Mean depth (coverage) in X
[x] Zero coverage (percent of genome not covered)
[x] Mapped reads in percent
[x] PCR Duplication
[ ] Q30 bases, Read 1
[ ] Q30 bases, Read 2

Some of these stats exist for our samples but should be put into the multiqc report.

pontushojer commented 3 years ago

Q30 bases are covered by FASTQC. Not number is outputted but from the plots 'Sequence Quality Histograms' and 'Per Sequence Quality Scores' you can overview the base qualities. I think this is sufficient for now.