Created
May 24, 2021 00:43
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| # where $1 is the sample name. eg sample-0112, for naming scheme sample-0112_merged.bam, etc. | |
| samtools mpileup \ | |
| -f nCoV-2019.reference.fasta \ | |
| --max-depth 1000 \ | |
| --positions nCoV-2019.reportable_region.bed \ | |
| ${1}_merged.bam -o ${1}_merged.mpileup | |
| java -jar VarScan.v2.4.3.jar mpileup2snp \ | |
| ${1}_merged.mpileup \ | |
| --min-coverage 50 \ | |
| --min-reads2 5 \ | |
| --min-var-freq 0.05 \ | |
| --p-value 0.99 \ | |
| --variants \ | |
| --output-vcf \ | |
| --strand-filter 0 \ | |
| > ${1}.raw_varscan_snvs.vcf | |
| java -jar VarScan.v2.4.3.jar mpileup2indel \ | |
| ${1}_merged.mpileup \ | |
| --min-coverage 50 \ | |
| --min-reads2 5 \ | |
| --min-var-freq 0.05 \ | |
| --p-value 0.99 \ | |
| --variants \ | |
| --output-vcf \ | |
| --strand-filter 0 \ | |
| > ${1}.raw_varscan_indel.vcf |
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