Merge branch 'master' of git.biohpc.swmed.edu:BICF/Astrocyte/process_scripts

alignment/markdups.sh

@@ -57,7 +57,7 @@ elif [ $algo == 'fgbio_umi' ]
 then
     module load fgbio bwa/intel/0.7.15
     samtools index -@ $SLURM_CPUS_ON_NODE ${sbam}
-    fgbio GroupReadsByUmi -s identity -i ${sbam} -o ${pair_id}.group.bam -e 0 -m 0
+    fgbio GroupReadsByUmi -s identity -i ${sbam} -o ${pair_id}.group.bam --family-size-histogram ${pair_id}.umihist.txt -e 0 -m 0
     fgbio CallMolecularConsensusReads -i ${pair_id}.group.bam -p consensus -M 1 -o ${pair_id}.consensus.bam -S ':none:'
     samtools index ${pair_id}.consensus.bam
     samtools fastq -1 ${pair_id}.consensus.R1.fastq -2 ${pair_id}.consensus.R2.fastq ${pair_id}.consensus.bam

variants/annotvcf.sh

@@ -23,7 +23,7 @@ done
 shift $(($OPTIND -1))
 
 source /etc/profile.d/modules.sh
-module load python/2.7.x-anaconda bedtools/2.26.0 samtools/1.6 snpeff/4.3q
+module load bedtools/2.26.0 samtools/1.6 snpeff/4.3q
 
 if [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh38/hisat_index' ]]
 then
@@ -32,8 +32,8 @@ fi
 
 if  [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh38' ]] 
 then
-    tabix ${unionvcf}
-    bcftools annotate -Oz -a ${index_path}/gnomad.txt.gz -h ${index_path}/gnomad.header -c CHROM,POS,REF,ALT,HG19_VARIANT,GNOMAD_HOM,GNOMAD_AF,AF_POPMAX -o ${pair_id}.gnomad.vcf.gz ${unionvcf}
+    tabix -f ${unionvcf}
+    bcftools annotate -Oz -a ${index_path}/gnomad.txt.gz -h ${index_path}/gnomad.header -c CHROM,POS,REF,ALT,GNOMAD_HOM,GNOMAD_AF,AF_POPMAX,GNOMAD_HG19_VARIANT -o ${pair_id}.gnomad.vcf.gz ${unionvcf}
     tabix ${pair_id}.gnomad.vcf.gz 
     bcftools annotate -Oz -a ${index_path}/repeat_regions.bed.gz -o ${pair_id}.repeat.vcf.gz --columns CHROM,FROM,TO,RepeatType -h /project/shared/bicf_workflow_ref/RepeatType.header ${pair_id}.gnomad.vcf.gz
     java -Xmx10g -jar $SNPEFF_HOME/snpEff.jar -no-downstream -no-upstream -no-intergenic -lof -c $SNPEFF_HOME/snpEff.config GRCh38.86 ${pair_id}.repeat.vcf.gz | java -jar $SNPEFF_HOME/SnpSift.jar annotate -id ${index_path}/dbSnp.vcf.gz -  | java -jar $SNPEFF_HOME/SnpSift.jar annotate -info CLNSIG,CLNDSDB,CLNDSDBID,CLNDBN,CLNREVSTAT,CLNACC ${index_path}/clinvar.vcf.gz - | java -jar $SNPEFF_HOME/SnpSift.jar annotate -info CNT ${index_path}/cosmic.vcf.gz - | java -Xmx10g -jar $SNPEFF_HOME/SnpSift.jar dbnsfp -v -db ${index_path}/dbNSFP.txt.gz - | bgzip > ${pair_id}.annot.vcf.gz
@@ -41,7 +41,7 @@ then
 else 
     if [[ $index_path == '/project/shared/bicf_workflow_ref/mouse/GRCm38' ]]
     then
-	snpeffvers='GRCh38.86'
+	snpeffvers='GRCm38.86'
     elif [[ $index_path == '/project/shared/bicf_workflow_ref/human/GRCh37' ]]
     then
 	snpeffvers='GRCh37.75'