fprintf(stderr, " -G FLOAT prior of an indel between two haplotypes (for -c) [%.4g]\n", d->ido->r_indel);
fprintf(stderr, " -I INT phred prob. of an indel in sequencing/prep. (for -c) [%d]\n", d->ido->q_indel);
fprintf(stderr, "\n");
+ fprintf(stderr, "Warning: Please use the `mpileup' command instead `pileup'. `Pileup' is deprecated!\n\n");
free(fn_list); free(fn_fa); free(d);
return 1;
}
if (use_orphan) mplp.flag &= ~MPLP_NO_ORPHAN;
if (argc == 1) {
fprintf(stderr, "\n");
- fprintf(stderr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
- fprintf(stderr, "Options: -f FILE reference sequence file [null]\n");
- fprintf(stderr, " -r STR region in which pileup is generated [null]\n");
- fprintf(stderr, " -l FILE list of positions (format: chr pos) [null]\n");
- fprintf(stderr, " -b FILE list of input BAM files [null]\n");
- fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
- fprintf(stderr, " -Q INT min base quality [%d]\n", mplp.min_baseQ);
- fprintf(stderr, " -q INT filter out alignment with MQ smaller than INT [%d]\n", mplp.min_mq);
- fprintf(stderr, " -d INT max per-BAM depth [%d]\n", mplp.max_depth);
- fprintf(stderr, " -L INT max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth);
- fprintf(stderr, " -P STR comma separated list of platforms for indels [all]\n");
- fprintf(stderr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
- fprintf(stderr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
- fprintf(stderr, " -h INT coefficient for homopolyer errors [%d]\n", mplp.tandemQ);
- fprintf(stderr, " -m INT minimum gapped reads for indel candidates [%d]\n", mplp.min_support);
- fprintf(stderr, " -F FLOAT minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac);
- fprintf(stderr, " -G FILE exclude read groups listed in FILE [null]\n");
- fprintf(stderr, " -6 quality is in the Illumina-1.3+ encoding\n");
- fprintf(stderr, " -A use anomalous read pairs in SNP/INDEL calling\n");
- fprintf(stderr, " -g generate BCF output\n");
- fprintf(stderr, " -u do not compress BCF output\n");
- fprintf(stderr, " -E extended BAQ for higher sensitivity but lower specificity\n");
- fprintf(stderr, " -B disable BAQ computation\n");
- fprintf(stderr, " -D output per-sample DP\n");
- fprintf(stderr, " -S output per-sample SP (strand bias P-value, slow)\n");
- fprintf(stderr, " -I do not perform indel calling\n");
+ fprintf(stderr, "Usage: samtools mpileup [options] in1.bam [in2.bam [...]]\n\n");
+ fprintf(stderr, "Input options:\n\n");
+ fprintf(stderr, " -6 assume the quality is in the Illumina-1.3+ encoding\n");
+ fprintf(stderr, " -A count anomalous read pairs\n");
+ fprintf(stderr, " -B disable BAQ computation\n");
+ fprintf(stderr, " -b FILE list of input BAM files [null]\n");
+ fprintf(stderr, " -d INT max per-BAM depth to avoid excessive memory usage [%d]\n", mplp.max_depth);
+ fprintf(stderr, " -E extended BAQ for higher sensitivity but lower specificity\n");
+ fprintf(stderr, " -f FILE faidx indexed reference sequence file [null]\n");
+ fprintf(stderr, " -G FILE exclude read groups listed in FILE [null]\n");
+ fprintf(stderr, " -l FILE list of positions (chr pos) or regions (BED) [null]\n");
+ fprintf(stderr, " -M INT cap mapping quality at INT [%d]\n", mplp.max_mq);
+ fprintf(stderr, " -r STR region in which pileup is generated [null]\n");
+ fprintf(stderr, " -q INT skip alignments with mapQ smaller than INT [%d]\n", mplp.min_mq);
+ fprintf(stderr, " -Q INT skip bases with baseQ/BAQ smaller than INT [%d]\n", mplp.min_baseQ);
+ fprintf(stderr, "\nOutput options:\n\n");
+ fprintf(stderr, " -D output per-sample DP in BCF (require -g/-u)\n");
+ fprintf(stderr, " -g generate BCF output (genotype likelihoods)\n");
+ fprintf(stderr, " -S output per-sample strand bias P-value in BCF (require -g/-u)\n");
+ fprintf(stderr, " -u generate uncompress BCF output\n");
+ fprintf(stderr, "\nSNP/INDEL genotype likelihoods options (effective with `-g' or `-u'):\n\n");
+ fprintf(stderr, " -e INT Phred-scaled gap extension seq error probability [%d]\n", mplp.extQ);
+ fprintf(stderr, " -F FLOAT minimum fraction of gapped reads for candidates [%g]\n", mplp.min_frac);
+ fprintf(stderr, " -h INT coefficient for homopolymer errors [%d]\n", mplp.tandemQ);
+ fprintf(stderr, " -I do not perform indel calling\n");
+ fprintf(stderr, " -L INT max per-sample depth for INDEL calling [%d]\n", mplp.max_indel_depth);
+ fprintf(stderr, " -m INT minimum gapped reads for indel candidates [%d]\n", mplp.min_support);
+ fprintf(stderr, " -o INT Phred-scaled gap open sequencing error probability [%d]\n", mplp.openQ);
+ fprintf(stderr, " -P STR comma separated list of platforms for indels [all]\n");
fprintf(stderr, "\n");
fprintf(stderr, "Notes: Assuming diploid individuals.\n\n");
return 1;
projects / samtools.git / blobdiff