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Commit 99a7f2e0 authored by Peter van 't Hof's avatar Peter van 't Hof
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parent 5a7743d9
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......@@ -77,7 +77,7 @@ object MpileupToVcf extends ToolCommand {
writer.println("##FORMAT=<ID=AFC,Number=A,Type=Integer,Description=\"Alternative Forward Reads\">")
writer.println("##FORMAT=<ID=ARC,Number=A,Type=Integer,Description=\"Alternative Reverse Reads\">")
writer.println("##FORMAT=<ID=SEQ-ERR,Number=.,Type=Float,Description=\"Probability to not be a sequence error with error rate " + commandArgs.seqError + "\">")
writer.println("##FORMAT=<ID=MA-SEQ-ERR,Number=1,Type=Float,Description=\"Probability to not be a sequence error with error rate " + commandArgs.seqError + "\">")
writer.println("##FORMAT=<ID=MA-SEQ-ERR,Number=1,Type=Float,Description=\"Minimal probability for all alternative alleles to not be a sequence error with error rate " + commandArgs.seqError + "\">")
writer.println("##FORMAT=<ID=GT,Number=1,Type=String,Description=\"Genotype\">")
writer.println("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t" + commandArgs.sample)
val inputStream = if (commandArgs.input != null) {
......
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