Commit a4c89a28 authored by Marwan ELKREWI's avatar Marwan ELKREWI
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Update SNP_calling_in_backcrossing_experiment.md

parent 10c406dc
......@@ -125,16 +125,16 @@ samtools mpileup -B Asex.sort.bam Sex.sort.bam > Asex_Sex.mpileup
```
### 9. Run Popoolation
```
java -ea -Xmx7g -jar Popoolation2/popoolation2_1201/mpileup2sync.jar --input Asex_Sex.mpileup --output Asex_Sex_java.sync --fastq-type sanger --min-qual 20 --threads 2
perl Popoolation2/popoolation2_1201/snp-frequency-diff.pl --input Asex_Sex_java.sync --output-prefix Asex_Sex --min-count 6 --min-coverage 50 --max-coverage 200
java -ea -Xmx7g -jar /Popoolation2/popoolation2_1201/mpileup2sync.jar --input Asex_Sex.mpileup --output Asex_Sex_java.sync --fastq-type sanger --min-qual 20 --threads 2
perl Popoolation2/popoolation2_1201/snp-frequency-diff.pl --input Asex_Sex_java.sync --output-prefix Asex_Sex --min-count 6 --min-coverage 10 --max-coverage 2000
per SNP
perl Popoolation2/popoolation2_1201/fst-sliding.pl --input Asex_Sex_java.sync --output Asex_Sex.persnp.fst --suppress-noninformative --min-count 2 --min-coverage 20 --max-coverage 1000 --min-covered-fraction 1 --window-size 1 --step-size 1 --pool-size 5:10
perl Popoolation2/popoolation2_1201/fst-sliding.pl --input Asex_Sex_java.sync --output Asex_Sex.persnp.fst --suppress-noninformative --min-count 2 --min-coverage 10 --max-coverage 2000 --min-covered-fraction 1 --window-size 1 --step-size 1 --pool-size 5:10
per 1kb
perl Popoolation2/popoolation2_1201/fst-sliding.pl --input Asex_Sex_java.sync --output Asex_Sex.1kb.fst --suppress-noninformative --min-count 2 --min-coverage 50 --max-coverage 1000 --min-covered-fraction 1 --window-size 1000 --step-size 1000 --pool-size 5:10
perl Popoolation2/popoolation2_1201/fst-sliding.pl --input Asex_Sex_java.sync --output Asex_Sex.1kb.min10.fst --suppress-noninformative --min-count 2 --min-coverage 10 --max-coverage 2000 --min-covered-fraction 1 --window-size 1000 --step-size 1000 --pool-size 5:10
```
### 10. R Script to make figures
......
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