2. out.html

[Cleiti]

• Leave multiQC plots in multiQC

• [x] create sarek_results.py making sarek_results.html

• add to local html:

• [x] text stats: -sarek_text_stats.py: add samtools stats alignment scores in percentages (from multiQC.html) -sarek_text_stats.py: delete dupvalues -when done: make a part sarek_results.html -delete sarek_text_stats.py

• [x] deduplicates from multiQC (has legend)

• [x] GC bias (#15)

• [ ] genotype concordance from vcf (variant calling, can do before annotation solved)?

---

• [ ] Picard on Bigyeast redo -> good amount of files or mistake somewhere?

• [ ] if good -> transfer all that part of pipeline to other data + runit + give to amanda

[Cleiti]

• [x] all files edited and set in right dirs for: smallYeast, upHorse, oupHorse, speciesmixHorse, speciesmixYeast, speciesmixHuman
• [x] picard.sh on smallYeast -> running
• [ ] picard.sh on upHorse -> running
• [ ] picard.sh on oupHorse -> running
• [ ] picard.sh on species mix Horse -> running
• [x] picard.sh on species mix Yeast -> running
• [x] picard.sh on species mix Human -> running
• [ ] GC_bias.R on smallYeast
• [ ] GC_bias.R on upHorse
• [ ] GC_bias.R on oupHorse
• [ ] GC_bias.R on species mix Horse
• [x] GC_bias.R on species mix Yeast
• [x] GC_bias.R on species mix Human
• [ ] sarek_results.py on smallYeast
• [ ] sarek_results.py on upHorse
• [ ] sarek_results.py on oupHorse
• [ ] sarek_results.py on species mix Horse
• [x] sarek_results.py on species mix Yeast
• [x] sarek_results.py on species mix Human
• [ ] folder sarek_results with html sent to amanda for: smallYeast, upHorse, oupHorse, speciesmixHorse, speciesmixYeast, speciesmixHuman