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src/call_var_main.c

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -660,9 +660,9 @@ static void call_var_usage(void) {//main usage
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fprintf(stderr, " chr1 100 (chr1:100-END)\n");
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fprintf(stderr, " chr1 100 200 (chr1:100-200)\n");
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fprintf(stderr, " --autosome Only call variants on autosomes [False]\n");
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fprintf(stderr, " e.g., human: chr1-22 or 1-22\n");
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fprintf(stderr, " e.g., human: chr{1-22} or 1-22\n");
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fprintf(stderr, " --autosome-XY Only call variants on autosomes and sex chromosomes [False]\n");
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fprintf(stderr, " e.g., human: chr1-22,chrXY or 1-22,XY\n");
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fprintf(stderr, " e.g., human: chr{1-22,XY} or 1-22,XY\n");
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fprintf(stderr, " -r --ref-idx FILE .fai index file for reference genome FASTA file, detect automaticaly if not provided [NULL]\n");
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// fprintf(stderr, " -b --out-bam STR output phased BAM file [NULL]\n");
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fprintf(stderr, " -n --sample-name STR sample name. 'RG/SM' in BAM header will be used if not provided [NULL]\n");

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