script terminal output log

01-SNPfilters/filtering.sh

@@ -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

README.md

 # 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