Commit defd337c authored by eboulanger's avatar eboulanger
Browse files

script terminal output log

parent 11a75552
......@@ -67,7 +67,7 @@ awk '/#/' DP3g95maf05.recode.vcf
# population level: vcffilter -s -f "AB > 0.25 & AB < 0.75 | AB < 0.01" DP3g95p5maf05.recode.vcf > DP3g95p5maf05.fil1.vcf
vcffilter -s -f "AB > 0.25 & AB < 0.75 | AB < 0.01" DP3g95maf05.recode.vcf > DP3g95maf05.fil1.vcf
# check how many were removed
DP3g95maf05.recode.vcf | wc -l
awk '!/#/' DP3g95maf05.recode.vcf | wc -l
awk '!/#/' DP3g95maf05.fil1.vcf | wc -l
# step 6 : filter out sites that have reads from both strands
......
# seaConnect--dataPrep
Scripts to prepare RADSeq data for analysis.
Scripts to prepare GBS data for analysis.
- filtering steps for dDocent SNP output
- outlier detection
- file conversions, subsetting and renaming
......@@ -27,6 +27,11 @@ cd ~/Documents/project_SEACONNECT/seaConnect--dataPrep/01-SNPfilters/
mkdir 01-Diplodus
mkdir 02-Mullus
```
start a log of the terminal output
```
script 01-Diplodus/filtering.log
script 02-Mullus/filtering.log
```
set the species-specific arguments for the script to run on
$1 = input file (specify path if not in current directory)
$2 = output folder
......@@ -35,6 +40,10 @@ set the species-specific arguments for the script to run on
bash filtering.sh ../00-rawData/01-Diplodus/sar_ddocent.vcf 01-Diplodus dip
bash filtering.sh ../00-rawData/02-Mullus/mullus.vcf 02-Mullus mul
```
when all steps are finished: finish the terminal output log
```
exit
```
### SNP filtering results for Mullus surmuletus
......
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