Commit 3fcc5a3d authored by Jacques Lagnel's avatar Jacques Lagnel
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update README

parent ad9a0638
......@@ -5,15 +5,15 @@
### 2) reads QC, fastq report
### 3) merges overlaping read and keep unmerged Paired end (R1 & R2)
### 4) mapping with bwa,
a) maps unmerged reads (PE)
b) maps merged reads
c) merge the 2 bam file
a) Maps unmerged reads (PE)
b) Maps merged reads
c) Merge the 2 bam file
### 5) mapping QC report (multiqc)
### 6) SNPs calling using GATK in parallel mode: reference splitted by sequences: #tasks=#samples X #chrs
#### a) GATK using "Best Practices Workflows" https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows
#### b) using hard filtering as outlined in GATK docs
#### https://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set
#### https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants
a) GATK using "Best Practices Workflows" https://gatk.broadinstitute.org/hc/en-us/sections/360007226651-Best-Practices-Workflows
b) Using hard filtering as outlined in GATK docs
https://gatkforums.broadinstitute.org/gatk/discussion/2806/howto-apply-hard-filters-to-a-call-set
https://gatk.broadinstitute.org/hc/en-us/articles/360035890471-Hard-filtering-germline-short-variants
......
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