Update test for minimap2 and add tests for vc module

tests/test_software.sh

@@ -15,9 +15,9 @@ PicardCommandLine -h
 breakdancer-max
 bam2cfg.pl -h
 sniffles --help
-#lumpy --help
-#lumpyexpress -h
-ngmlr --help
+lumpy --help
+lumpyexpress -h
+minimap2
 
 hisat2 -h
 kallisto 

tests/test_variant_calling.sh

@@ -0,0 +1,54 @@
+##Introduction
+cd /home/manager/course_data/variant_calling/data
+samtools --help
+bcftools --help
+igv &
+
+##Calling variants
+pwd
+ls -lh
+samtools mpileup -f GRCm38_68.19.fa A_J.bam | head
+samtools mpileup -f GRCm38_68.19.fa A_J.bam | grep 10001994
+bcftools mpileup -f GRCm38_68.19.fa A_J.bam | head
+bcftools mpileup -f GRCm38_68.19.fa A_J.bam | bcftools call -m | head
+bcftools mpileup -f GRCm38_68.19.fa A_J.bam | bcftools call -mv | head
+bcftools mpileup -a ?
+bcftools mpileup -a AD -f GRCm38_68.19.fa A_J.bam -Ou | bcftools call -mv -o out.vcf
+grep 10001994 out.vf
+grep 10003649 out.vcf
+
+##Filtering Variants
+bcftools query --format 'POS=%POS\n' out.vcf | head
+bcftools query -f'%POS %REF,%ALT\n' out.vcf | head
+bcftools query -f'%POS %QUAL [%GT %AD] %REF %ALT\n' out.vcf | head
+bcftools query -f'%POS %QUAL [%GT %AD] %REF %ALT\n' -i'QUAL>=30' out.vcf | head
+bcftools query -f'%POS %QUAL [%GT %AD] %REF %ALT\n' -i'QUAL>=30 && type="snp"' out.vcf | head
+##Exercises
+bcftools query -f'%POS %QUAL [%GT %AD] %REF %ALT\n' -i'QUAL>=30 && type="snp" && AD[*:1]>=25' out.vcf | head
+bcftools stats out.vcf | grep TSTV | cut -f5
+bcftools stats -i'QUAL>=30 && AD[*:1]>=25' out.vcf | grep TSTV | cut -f5
+bcftools stats -e'QUAL>=30 && AD[*:1]>=25' out.vcf | grep TSTV | cut -f5
+bcftools stats -i 'GT="het"' out.vcf | grep TSTV | cut -f5
+bcftools filter -s LowQual -i'QUAL>=30 && AD[*:1]>=25' -g8 -G10 out.vcf -o out.flt.vcf
+bcftools norm -f GRCm38_68.19.fa out.flt.vcf -o out.flt.norm.vcf
+
+##Multisample calling
+ls *.bam
+bcftools mpileup -a AD -f GRCm38_68.19.fa *.bam -Ou | bcftools call -mv -Ob -o multi.bcf 
+bcftools index multi.bcf
+bcftools filter -s LowQual -i'QUAL>=30 && AD[*:1]>=25' -g8 -G10 multi.bcf -Ob -o multi.filt.bcf
+bcftools index multi.filt.bcf
+#Exercises
+bcftools stats multi.filt.bcf | grep TSTV | cut -f5 (raw calls)
+bcftools stats -i 'FILTER="PASS"' multi.filt.bcf | grep TSTV | cut -f5 (only filtered set)
+bcftools stats -e 'FILTER="PASS"' multi.filt.bcf | grep TSTV | cut -f5
+
+##Visualising variants
+##Test manually
+bcftools view -H -r 19:10001946 multi.filt.bcf
+bcftools view -H -r 19:10072443 multi.filt.bcf
+
+##Annotating variants
+bcftools view -i 'FILTER="PASS"' multi.filt.bcf | bcftools csq -p m -f GRCm38_68.19.fa -g Mus_musculus.part.gff3.gz -Ob -o multi.filt.annot.bcf
+bcftools index multi.filt.annot.bcf
+bcftools query -f '%BCSQ' -r 19:10088937 multi.filt.annot.bcf