added SNP and INDEL calling

README.md

@@ -62,8 +62,83 @@ _used software:_
 
 ## SNP and INDEL calling
 
+For SNP and INDEL calling the BAM files were processed with 'samtools mpileup' and 'bcftools call' with relaxed quality options to retain information in CNV regions.
+Due to the amount of data first mpileup files were generated for each BAM file and merged with 'bcftools merge'. After merging mpileup files, 'bcftools call' was used to generate the final VCF file.
+
+samtools mpileup | bcftools call example for the population _Mus musculus musculus AFG_:
+```
+#example for population Mmm_AFG:
+#
+#used BAM files:
+#
+#AFG1_396.bam
+#AFG2_413.bam
+#AFG3_416.bam
+#AFG4_424.bam
+#AFG5_435.bam
+#AFG6_444.bam
+
+#generating indiviual mpileup files for each BAM file
+
+$REFERENCE=mm10.fasta
+
+INPUT1=AFG1_396.bam
+INPUT2=AFG2_413.bam
+INPUT3=AFG3_416.bam
+INPUT4=AFG4_424.bam
+INPUT5=AFG5_435.bam
+INPUT6=AFG6_444.bam
+
+samtools mpileup -q 0 -Q 10 -A -d 99999 -t DP,AD,ADF,ADR -vf $REFERENCE -o $INPUT1".mpileup.q0Q10.vcf" $INPUT1
+samtools mpileup -q 0 -Q 10 -A -d 99999 -t DP,AD,ADF,ADR -vf $REFERENCE -o $INPUT2".mpileup.q0Q10.vcf" $INPUT2
+samtools mpileup -q 0 -Q 10 -A -d 99999 -t DP,AD,ADF,ADR -vf $REFERENCE -o $INPUT3".mpileup.q0Q10.vcf" $INPUT3
+samtools mpileup -q 0 -Q 10 -A -d 99999 -t DP,AD,ADF,ADR -vf $REFERENCE -o $INPUT4".mpileup.q0Q10.vcf" $INPUT4
+samtools mpileup -q 0 -Q 10 -A -d 99999 -t DP,AD,ADF,ADR -vf $REFERENCE -o $INPUT5".mpileup.q0Q10.vcf" $INPUT5
+samtools mpileup -q 0 -Q 10 -A -d 99999 -t DP,AD,ADF,ADR -vf $REFERENCE -o $INPUT6".mpileup.q0Q10.vcf" $INPUT6
+
+bgzip $INPUT1".mpileup.q0Q10.vcf"
+bgzip $INPUT2".mpileup.q0Q10.vcf"
+bgzip $INPUT3".mpileup.q0Q10.vcf"
+bgzip $INPUT4".mpileup.q0Q10.vcf"
+bgzip $INPUT5".mpileup.q0Q10.vcf"
+bgzip $INPUT6".mpileup.q0Q10.vcf"
+
+tabix $INPUT1".mpileup.q0Q10.vcf.gz"
+tabix $INPUT2".mpileup.q0Q10.vcf.gz"
+tabix $INPUT3".mpileup.q0Q10.vcf.gz"
+tabix $INPUT4".mpileup.q0Q10.vcf.gz"
+tabix $INPUT5".mpileup.q0Q10.vcf.gz"
+tabix $INPUT6".mpileup.q0Q10.vcf.gz"
+
+#merge individual mpileup files
+
+MPILEUPLIST=AFG.mpileup.list
+
+echo $INPUT1".mpileup.q0Q10.vcf.gz" >> $MPILEUPLIST
+echo $INPUT2".mpileup.q0Q10.vcf.gz" >> $MPILEUPLIST
+echo $INPUT3".mpileup.q0Q10.vcf.gz" >> $MPILEUPLIST
+echo $INPUT4".mpileup.q0Q10.vcf.gz" >> $MPILEUPLIST
+echo $INPUT5".mpileup.q0Q10.vcf.gz" >> $MPILEUPLIST
+echo $INPUT6".mpileup.q0Q10.vcf.gz" >> $MPILEUPLIST
+
+MPILEUPOUTPUT=AFG.mpileup.q0Q10.vcf.gz
+
+bcftools merge -m all -O z -o $MPILEUPOUTPUT -l $MPILEUPLIST
+
+#call SNP and INDEL
+
+OUTPUT=AFG.mpileup.q0Q10.bcfcall.mv.vcf.gz
+
+bcftools call -O z -f GQ -m -v -o $OUTPUT $MPILEUPOUTPUT
+```
+
 _used software:_
 
++ samtools 1.3.1-36-g613501f (using htslib 1.3.1-59-g0f2a88a)
++ bcftools 1.3.1-39-gd797e86 (using htslib 1.3.1-59-g0f2a88a)
++ bgzip v1.3
++ tabix v1.3
+
 ## K80 distance calculation
 
 ### Get population specific SNPs