Commit 5e7b4cdf authored by Marwan ELKREWI's avatar Marwan ELKREWI
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Update SNP_calling_in_backcrossing_experiment.md

parent 3d2f4be7
......@@ -155,8 +155,8 @@ samtools mpileup -B -d 10000000 -f Artemia_sinica_genome_29_12_2021.fasta -b
```
### 11. Build vcf (raw) for downstream supplemental analyses
```
java -jar VarScan.v2.4.3.jar mpileup2snp Asex.Sex.sample.pileup --min-coverage 5 --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 5 --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
java -jar VarScan.v2.4.3.jar mpileup2snp Asex.Sex.sample.pileup --min-coverage 5 --min-avg-qual 10 --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 5 --min-avg-qual 10 --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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