How to output VarsScan variant calling results in a .tab or txt/csv file?
How to output VarsScan variant calling results in a .tab or txt/csv file? I run code line
samtools mpileup -f H37Rv_reference.fa ls_sorted.bam | java -jar VarScan.jar pileup2snp --output-file varscan_results.tab
but there is not saved output, it says:
1115568 bases in pileup file 979731 met minimum coverage of 8x 7055 SNPs predicted
how to save results in a file?
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vassialkalive23 •
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You are using mpileup with pileup2snp, did you try using with mpileup2snp?