NGS-Var2018 Exercise.3

[ Main_Page | Hands-on_introduction_to_NGS_variant_analysis-2018 | NGS-Var2018 Exercise.2 | NGS-Var2018 Exercise.4 ]

---

BWA mapping QC using Picard tools, and Qualimap

Each mapping is unique and can be biased by many unknown factors. Performing QC is essential in each experiment to avoid carryover of errors to the downstream analyses.

 

Perform mapping QC using Picard CollectMultipleMetrics

Picard tools include a number of valuable QC programs that can be used separately or with one single command triggering multiple tests as shown next.

• start the Picard.CollectMultipleMetrics module and link the last BAM file from the previous exercise and to the human UCSC.hg38 reference

• wait and review the PDF and TXT results from the list

PDF results for the 1% and 10% data are available in ex3-files

 

 

Perform integrated BAM QC with the GenePattern Qualimap module

• select the QualimapBamQC module and fill the parameters as shown

• run and wait for results

• the results of the analysis of the 1% sample are HERE
• the results of the analysis of the 10% sample are HERE

 

download exercise files

Download exercise files here

Use the right application to open the files present in ex3-files

---

References:

---

[ Main_Page | Hands-on_introduction_to_NGS_variant_analysis-2018 | NGS-Var2018 Exercise.4 ]

---