Details on custom VerifyBamID panel

docs/Software_installation.md

@@ -48,6 +48,65 @@ Increase JVM memory for GATK in galaxy/bcbio_system.yaml
     jvm_opts: ["-Xms500m", "-Xmx5g"]
 ```
 
+### Verifybamid custom panel for exomes
+
+```
+source /home/u035/project/scripts/trio_whole_exome_config.sh
+
+mkdir /home/u035/project/software/install/1000G_phase3_hg38
+cd /home/u035/project/software/install/1000G_phase3_hg38
+
+# download the 1000 Genomes autosomes + X site VCFs
+for ((i = 1; i <= 22; i = i + 1))
+do
+  wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr${i}.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz;
+  wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chr${i}.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz.tbi
+done
+wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chrX.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz
+wget ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL/ALL.chrX.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.vcf.gz.tbi
+cd ..
+
+# create bare to prefixed chromosome map
+for ((i = 1; i <= 22; i = i + 1))
+do
+  echo $i "chr"$i >> chr_prefix_map.txt
+done
+echo chrX >> chr_prefix_map.txt
+
+# use the TWIST kit to subset the variants and add the chr prefix at the same time
+for file in 1000G_phase3_hg38/*vcf.gz
+do
+  bname=`basename $file`
+  bcftools view -R /home/u035/project/resources/Twist_Exome_Target_hg38.bed -m2 -M2 -v snps -i 'AF >= 0.01' $file | bcftools annotate --rename-chrs chr_prefix_map.txt | bgzip -c > ${bname%.vcf.gz}.biallelic.snps.m\
+inAF0.01.vcf.gz
+  tabix ${bname%.vcf.gz}.biallelic.snps.minAF0.01.vcf.gz
+done
+
+# concatenate all the files in the correct order
+bcftools concat -o ALL.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.chr.biallelic.snps.minAF0.01.vcf.gz -O z \
+  ALL.chr[1-9].shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.chr.biallelic.snps.minAF0.01.vcf.gz \
+  ALL.chr[12][0-9].shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.chr.biallelic.snps.minAF0.01.vcf.gz \
+  ALL.chrX.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.chr.biallelic.snps.minAF0.01.vcf.gz
+tabix ALL.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.chr.biallelic.snps.minAF0.01.vcf.gz
+
+# use VerifyBamID to create the new panel
+/home/u035/project/software/bcbio/anaconda/share/verifybamid2-1.0.6-0/VerifyBamID \
+  --RefVCF ALL.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.chr.biallelic.snps.minAF0.01.vcf.gz
+  --Reference bcbio-1.1.5/genomes/Hsapiens/hg38/seq/hg38.fa
+
+# rename the files to the correct format
+mv ALL.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.chr.biallelic.snps.minAF0.01.vcf.gz.bed 1000g.phase3.100k.b38.vcf.gz.dat.bed
+mv ALL.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.chr.biallelic.snps.minAF0.01.vcf.gz.mu 1000g.phase3.100k.b38.vcf.gz.dat.mu
+mv ALL.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.chr.biallelic.snps.minAF0.01.vcf.gz.PC 1000g.phase3.100k.b38.vcf.gz.dat.V
+mv ALL.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.chr.biallelic.snps.minAF0.01.vcf.gz.UD 1000g.phase3.100k.b38.vcf.gz.dat.UD
+
+# move them into the correct location, backing up the original resource folder
+cd /home/u035/project/software/bcbio/anaconda/share/verifybamid2-1.0.6-0
+mv resource resource.bak
+mkdir resource
+mv /home/u035/project/software/install/1000G_phase3_hg38/1000g.phase3.100k.b38* resource/
+```
+
 ## VASE
 
 VASE was installed following the instructions at https://github.com/david-a-parry/vase, downloaded 27 August 2020.