call_SNPs_with_GATK: call SNPs with GATK
In abshah/RADseqR:
Description
call SNPs with GATK
Usage
1
call_SNPs_with_GATK(ref_fasta, bam_with_rg, Threads, output_vcf, java_mem)
Arguments
ref_fasta
reference genome or contigs (in fasta format)
bam_with_rg
BAM input file with full headers
Threads
number of threads to run (depends on server resources)
output_vcf
specify the output file (in VCF format)
java_mem
set memory usage for SNP calling using GATK
abshah/RADseqR documentation built on May 10, 2019, 5:08 a.m.
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Description
call SNPs with GATK
Usage
1 | call_SNPs_with_GATK(ref_fasta, bam_with_rg, Threads, output_vcf, java_mem)
|
Arguments
ref_fasta |
reference genome or contigs (in fasta format) |
bam_with_rg |
BAM input file with full headers |
Threads |
number of threads to run (depends on server resources) |
output_vcf |
specify the output file (in VCF format) |
java_mem |
set memory usage for SNP calling using GATK |
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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