call SNPs with GATK
1 | call_SNPs_with_GATK(ref_fasta, bam_with_rg, Threads, output_vcf, java_mem)
|
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 |
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