add run sscocaller

README.md

@@ -7,7 +7,7 @@ submit-wgetSRAFastqdump.sh for downloading sra files from GEO and dumping into f
 
 ### Step2 run alignment
 
-run_alignment.snk is a snakemake file which contains rules/steps for preprocessing the 
+`run_alignment.snk` is a snakemake file which contains rules/steps for preprocessing the 
 fastq reads and mapping reads to the mouse reference genome mm10
 
 ### Step3 subsample reads
@@ -24,7 +24,7 @@ Refer to steps defined in `run_subsample.snk`.
 `samtools` was used for merge CB-taged reads from all single sperm to one BAM file. See
 `submit-mergeBams.sh`
 
-### Step5 Findg informative SNP markers
+### Step5 Finding informative SNP markers
 
 The informative SNP markers are those SNPs which differ between the two mouse stains
 that were used to generate the F1 hybrid mouse (CAST and BL6). The following steps were
@@ -35,4 +35,9 @@ mouse individual using GATK HaplotypeCaller. Only the HET SNPs with `MQ>50` AND
 `DP>10` AND `DP<80` were kept.
 The SNPs were further filtered to only keep the positions which have been called 
 as Homo_alternative `CAST_EiJ.mgp.v5.snps.dbSNP142.vcf.gz` downloaded from the 
-dbsnp database from Mouse Genome Project.
\ No newline at end of file
+dbsnp database from Mouse Genome Project.
+
+## Running sscocaller
+
+`run_sscocaller.snk` defines the snakemake rule for running sscocaller for each chromosome.
+

run_sscocaller.snk

+# run sscocaller for merged bams
+
+
+rule all:
+    input: expand("sscocaller/hinch/hinch_{chr}_altCount.mtx",chr= ["chr1","chr2","chr3","chr4","chr5","chr6","chr7","chr8","chr9","chr10","chr11","chr12","chr13","chr14","chr15","chr16","chr17","chr18","chr19"])
+    
+
+rule run_sscocaller:
+    input:
+        mergedBam = "output/alignment/mergedBam/mergedAll.bam",
+        vcfRef="output/variants/denovoVar/SRR8454653.mkdup.sort.rg.filter.snps.castVar.vcf.gz",
+        bcFile="output/alignment/mergedBam/mergedAll.bam.barcodes.txt"
+    output: 
+        "output/sscocaller/hinch/hinch_{chr}_altCount.mtx"
+    threads: 4
+    benchmark:
+        "benchmarks/mergedAll.{chr}.sscocaller.benchmark.txt"
+    resources:
+        cpus = 4,
+        mem = 20480
+    shell:
+        """
+            /mnt/mcfiles/rlyu/Projects/sscocaller/src/sscocaller --threads {threads} --chrom {wildcards.chr} --chrName chr {input.mergedBam} {input.vcfRef} {input.bcFile} --maxTotalReads 150 --maxDP 10 sscocaller/hinch/hinch_
+        """