Commit 10c406dc authored by Marwan ELKREWI's avatar Marwan ELKREWI
Browse files

Update SNP_calling_in_backcrossing_experiment.md

parent f33d56d6
......@@ -3,12 +3,6 @@ Samples 16-20 are asexuals, 21-30 are putative sexuals.
The same parameters were run for asexuals and sexuals, unless stated otherwise.
Steps 1-6 are processing for all analyses.
Steps 7-10 are the processing for the Pooled Analysis (Popoolation) used in the main text.
Steps 11-12 Pipeline for individual-based analyses - produces the raw VCF for downstream analysis in the supplement.
### 1. Subset reads for the pooled analysis
Let's make sure we start with the same number of reads per female in each pool (asexuals and controls).
......@@ -151,16 +145,3 @@ infile2 = Asex_Sex.persnp.fst.modified.input.txt (FST per SNP)
infile1 = Asex_Sex.1kb.try3.fst.modifiedinput.txt (FST per 1kb)
## Individual-based analyses
### 11. Make pileup for indvidual-based analyses
```
samtools index Artemia_sinica_genome_29_12_2021.fasta
samtools mpileup -B -d 10000000 -f Artemia_sinica_genome_29_12_2021.fasta -b Asex.Sex.bamfilelist.txt > Asex.Sex.sample.pileup
```
### 12. Build vcf (raw) for downstream supplemental analyses
```
java -jar VarScan.v2.4.3.jar mpileup2snp Asex.Sex.sample.pileup --min-coverage 10 --min-avg-qual 20 --strand-filter 1 --p-value 0.05 --min-var-freq 0.15 --min-freq-for-hom 0.85 --min-reads2 3 --output-vcf > Asex.Sex.vcf
java -jar VarScan.v2.4.3.jar mpileup2cns Asex.Sex.sample.pileup --min-coverage 10 --min-avg-qual 20 --strand-filter 1 --p-value 0.05 --min-var-freq 0.15 --min-freq-for-hom 0.85 --min-reads2 3 --output-vcf > Asex.Sex.cns
```
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