postdoc/Caller_VarScan.sh at master · cdbope/postdoc · GitHub

1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
#!/bin/bash
#PBS -N VC_GATK
#PBS -W group_list=largeq
#PBS -q large
#PBS -P CBBI0818
#PBS -l select=20:ncpus=24
#PBS -l walltime=96:00:00

. /mnt/lustre/groups/CBBI0818/NOELLE/config.txt

DBSNPVCF=${dbsnp}

java -jar VarScan.v2.3.9.jar mpileup2snp sampleX.bcf > sampleX.snvs.txt \
#java -jar VarScan.v2.3.9.jar mpileup2indels sampleX.bcf > sampleX.indels.txt


#Initial Cov samples
java -jar GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R ${REF}ucsc.hg19.fasta \
-stand call conf 30.0 stand emit conf 10.0 \
--dbsnp $DBSNPVCF \
#-L target.bed \
-I ${BAM}NEW/${ANC}/${ANC}_${CHR}.realign.final.bam \
-o ${VCF}GATK/GATK_Calls.vcf

#Initial Cov Golden
java -jar GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R ${REF}ucsc.hg19.fasta \
-stand call conf 30.0 stand emit conf 10.0 \
--dbsnp $DBSNPVCF \
#-L target.bed \
-I ${outsim}NEW/${ANC}/${ANC}_${CHR}_sim_reads_golden.bam \
-o ${VCF}GATK/GATK_Calls_Golden.vcf

#Altered Cov samples
java -jar GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R ${REF}ucsc.hg19.fasta \
-stand call conf 30.0 stand emit conf 10.0 \
--dbsnp $DBSNPVCF \
#-L target.bed \
-I ${BAM}NEW/${ANC}/${ANC}_${CHR}_altcov.realign.final.bam \
-o ${VCF}GATK/GATK_Calls_altcov.vcf


#Altered Cov Golden
#Initial Cov Golden
java -jar GenomeAnalysisTK.jar \
-T HaplotypeCaller \
-R ${REF}ucsc.hg19.fasta \
-stand call conf 30.0 stand emit conf 10.0 \
--dbsnp $DBSNPVCF \
#-L target.bed \
-I ${outsim}NEW/${ANC}/${ANC}_${CHR}_sim_reads_altcov_golden.bam \
-o ${VCF}GATK/GATK_Calls_altcov_Golden.vcf