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utilities/numberReadsFastqGz.command

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+# 100720
+# returns number of reads in a fastq file
+
+# usage: numberReadsFastq.command XXX.fastq
+
+#!/bin/bash
+
+FASTQGZ="$1"
+
+zcat < $FASTQGZ | echo $((`wc -l`/4))

utilities/runSnifflesloop.command

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+#!/bin/bash
+
+# run Sniffles on a folder of BAM files
+
+mkdir SVs_sniffles/vcf
+
+for i in promoterbamfilt/*.bam # loop thru files in directory that finish by .bam
+do
+
+  BAM="$i"
+
+  PDG="$(echo "$BAM" | cut -d'_' -f 1 | cut -d'/' -f 2)" # everything before '_', then everything after '/'
+  # e.g. promoterbamfilt/55052_promoterSnif.vcf >> promoterbamfilt/55052, then 55052
+
+  VCF="$(echo $"SVs_sniffles/vcf/"$PDG$"_promoterSnif.vcf")"
+
+
+  echo "---- [ SNIFFING PROMOTER "$" $BAM ] ----"
+
+  sniffles --mapped_reads "$BAM" \
+      --vcf "$VCF" \
+      --genotype \
+      --min_support 10 \
+      --min_length 10 \
+      --max_distance 50
+
+done
+
+######
+
+for i in bamfilt/*.bam # loop thru files in directory that finish by .bam
+do
+
+  BAM="$i"
+
+  PDG="$(echo "$BAM" | cut -d'_' -f 1 | cut -d'/' -f 2)" # everything before '_', then everything after '/'
+  # e.g. bamfilt/55052_promoterSnif.vcf >> promoterbamfilt/55052, then 55052
+
+  VCF="$(echo $"SVs_sniffles/vcf/"$PDG$"_bodySnif.vcf")"
+
+  echo "---- [ SNIFFING GENEBODY "$" $BAM ] ----"
+
+  sniffles --mapped_reads "$BAM" \
+      --vcf "$VCF" \
+      --genotype \
+      --min_support 300 \
+      --min_length 20 \
+      --max_distance 50
+
+done