Program options for bcftools: Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs) Version: 1.13 (using htslib 1.13) Usage: bcftools [--version|--version-only] [--help] Commands: -- Indexing index index VCF/BCF files -- VCF/BCF manipulation annotate annotate and edit VCF/BCF files concat concatenate VCF/BCF files from the same set of samples convert convert VCF/BCF files to different formats and back isec intersections of VCF/BCF files merge merge VCF/BCF files files from non-overlapping sample sets norm left-align and normalize indels plugin user-defined plugins query transform VCF/BCF into user-defined formats reheader modify VCF/BCF header, change sample names sort sort VCF/BCF file view VCF/BCF conversion, view, subset and filter VCF/BCF files -- VCF/BCF analysis call SNP/indel calling consensus create consensus sequence by applying VCF variants cnv HMM CNV calling csq call variation consequences filter filter VCF/BCF files using fixed thresholds gtcheck check sample concordance, detect sample swaps and contamination mpileup multi-way pileup producing genotype likelihoods roh identify runs of autozygosity (HMM) stats produce VCF/BCF stats Most commands accept VCF, bgzipped VCF, and BCF with the file type detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most but not all situations. ---------------------------------------------- Program options for bcftools_index: [E::main_vcfindex] must specify an output path for index file when reading VCF/BCF from stdin index: invalid option -- 'h' About: Index bgzip compressed VCF/BCF files for random access. Usage: bcftools index [options] | Indexing options: -c, --csi generate CSI-format index for VCF/BCF files [default] -f, --force overwrite index if it already exists -m, --min-shift INT set minimal interval size for CSI indices to 2^INT [14] -o, --output FILE optional output index file name -t, --tbi generate TBI-format index for VCF files --threads INT use multithreading with INT worker threads [0] Stats options: -n, --nrecords print number of records based on existing index file -s, --stats print per contig stats based on existing index file ---------------------------------------------- Program options for samtools_sort: samtools sort: failed to read header from "-" sort: invalid option -- 'h' Usage: samtools sort [options...] [in.bam] Options: -l INT Set compression level, from 0 (uncompressed) to 9 (best) -m INT Set maximum memory per thread; suffix K/M/G recognized [768M] -n Sort by read name -t TAG Sort by value of TAG. Uses position as secondary index (or read name if -n is set) -o FILE Write final output to FILE rather than standard output -T PREFIX Write temporary files to PREFIX.nnnn.bam --no-PG do not add a PG line --input-fmt-option OPT[=VAL] Specify a single input file format option in the form of OPTION or OPTION=VALUE -O, --output-fmt FORMAT[,OPT[=VAL]]... Specify output format (SAM, BAM, CRAM) --output-fmt-option OPT[=VAL] Specify a single output file format option in the form of OPTION or OPTION=VALUE --reference FILE Reference sequence FASTA FILE [null] -@, --threads INT Number of additional threads to use [0] --verbosity INT Set level of verbosity ---------------------------------------------- Program options for bcftools_call: Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid Expected -c or -m option About: SNP/indel variant calling from VCF/BCF. To be used in conjunction with bcftools mpileup. This command replaces the former "bcftools view" caller. Some of the original functionality has been temporarily lost in the process of transition to htslib, but will be added back on popular demand. The original calling model can be invoked with the -c option. Usage: bcftools call [options] File format options: --no-version Do not append version and command line to the header -o, --output FILE Write output to a file [standard output] -O, --output-type b|u|z|v Output type: 'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v] --ploidy ASSEMBLY[?] Predefined ploidy, 'list' to print available settings, append '?' for details [2] --ploidy-file FILE Space/tab-delimited list of CHROM,FROM,TO,SEX,PLOIDY -r, --regions REGION Restrict to comma-separated list of regions -R, --regions-file FILE Restrict to regions listed in a file -s, --samples LIST List of samples to include [all samples] -S, --samples-file FILE PED file or a file with an optional column with sex (see man page for details) [all samples] -t, --targets REGION Similar to -r but streams rather than index-jumps -T, --targets-file FILE Similar to -R but streams rather than index-jumps --threads INT Use multithreading with INT worker threads [0] Input/output options: -A, --keep-alts Keep all possible alternate alleles at variant sites -a, --annotate LIST Optional tags to output (lowercase allowed); '?' to list available tags -F, --prior-freqs AN,AC Use prior allele frequencies, determined from these pre-filled tags -G, --group-samples FILE|- Group samples by population (file with "sample\tgroup") or "-" for single-sample calling. This requires FORMAT/QS or other Number=R,Type=Integer tag such as FORMAT/AD --group-samples-tag TAG The tag to use with -G, by default FORMAT/QS and FORMAT/AD are checked automatically -g, --gvcf INT,[...] Group non-variant sites into gVCF blocks by minimum per-sample DP -i, --insert-missed Output also sites missed by mpileup but present in -T -M, --keep-masked-ref Keep sites with masked reference allele (REF=N) -V, --skip-variants TYPE Skip indels/snps -v, --variants-only Output variant sites only Consensus/variant calling options: -c, --consensus-caller The original calling method (conflicts with -m) -C, --constrain STR One of: alleles, trio (see manual) -m, --multiallelic-caller Alternative model for multiallelic and rare-variant calling (conflicts with -c) -n, --novel-rate FLOAT,[...] Likelihood of novel mutation for constrained trio calling, see man page for details [1e-8,1e-9,1e-9] -p, --pval-threshold FLOAT Variant if P(ref|D) [out.index] Options: -b Generate BAI-format index for BAM files [default] -c Generate CSI-format index for BAM files -m INT Set minimum interval size for CSI indices to 2^INT [14] -@ INT Sets the number of threads [none] index: invalid option -- 'h' Usage: samtools index [-bc] [-m INT] [out.index] Options: -b Generate BAI-format index for BAM files [default] -c Generate CSI-format index for BAM files -m INT Set minimum interval size for CSI indices to 2^INT [14] -@ INT Sets the number of threads [none] ---------------------------------------------- Program options for bcftools_view: Failed to read from standard input: unknown file type Failed to read from standard input: unknown file type ---------------------------------------------- Program options for bcftools_mpileup: Usage: bcftools mpileup [options] in1.bam [in2.bam [...]] Input options: -6, --illumina1.3+ quality is in the Illumina-1.3+ encoding -A, --count-orphans do not discard anomalous read pairs -b, --bam-list FILE list of input BAM filenames, one per line -B, --no-BAQ disable BAQ (per-Base Alignment Quality) -C, --adjust-MQ INT adjust mapping quality [0] -D, --full-BAQ Apply BAQ everywhere, not just in problematic regions -d, --max-depth INT max raw per-file depth; avoids excessive memory usage [250] -E, --redo-BAQ recalculate BAQ on the fly, ignore existing BQs -f, --fasta-ref FILE faidx indexed reference sequence file --no-reference do not require fasta reference file -G, --read-groups FILE select or exclude read groups listed in the file -q, --min-MQ INT skip alignments with mapQ smaller than INT [0] -Q, --min-BQ INT skip bases with baseQ/BAQ smaller than INT [1] --max-BQ INT limit baseQ/BAQ to no more than INT [60] --delta-BQ INT Use neighbour_qual + INT if less than qual [30] -r, --regions REG[,...] comma separated list of regions in which pileup is generated -R, --regions-file FILE restrict to regions listed in a file --ignore-RG ignore RG tags (one BAM = one sample) --rf, --incl-flags STR|INT required flags: skip reads with mask bits unset [] --ff, --excl-flags STR|INT filter flags: skip reads with mask bits set [UNMAP,SECONDARY,QCFAIL,DUP] -s, --samples LIST comma separated list of samples to include -S, --samples-file FILE file of samples to include -t, --targets REG[,...] similar to -r but streams rather than index-jumps -T, --targets-file FILE similar to -R but streams rather than index-jumps -x, --ignore-overlaps disable read-pair overlap detection --seed INT random number seed used for sampling deep regions [0] Output options: -a, --annotate LIST optional tags to output; '?' to list available tags [] -g, --gvcf INT[,...] group non-variant sites into gVCF blocks according to minimum per-sample DP --no-version do not append version and command line to the header -o, --output FILE write output to FILE [standard output] -O, --output-type TYPE 'b' compressed BCF; 'u' uncompressed BCF; 'z' compressed VCF; 'v' uncompressed VCF [v] -U, --mwu-u use older probability scale for Mann-Whitney U test --threads INT use multithreading with INT worker threads [0] SNP/INDEL genotype likelihoods options: -X, --config STR Specify platform specific profiles (see below) -e, --ext-prob INT Phred-scaled gap extension seq error probability [20] -F, --gap-frac FLOAT minimum fraction of gapped reads [0.05] -h, --tandem-qual INT coefficient for homopolymer errors [500] -I, --skip-indels do not perform indel calling -L, --max-idepth INT maximum per-file depth for INDEL calling [250] -m, --min-ireads INT minimum number gapped reads for indel candidates [2] -M, --max-read-len INT maximum length of read to pass to BAQ algorithm [500] -o, --open-prob INT Phred-scaled gap open seq error probability [40] -p, --per-sample-mF apply -m and -F per-sample for increased sensitivity -P, --platforms STR comma separated list of platforms for indels [all] --ar, --ambig-reads STR What to do with ambiguous indel reads: drop,incAD,incAD0 [drop] --indel-bias FLOAT Raise to favour recall over precision [1.00] Configuration profiles activated with -X, --config: 1.12: -Q13 -h100 -m1 -F0.002 illumina: [ default values ] ont: -B -Q5 --max-BQ 30 -I [also try eg |bcftools call -P0.01] pacbio-ccs: -D -Q5 --max-BQ 50 -F0.1 -o25 -e1 --delta-BQ 10 -M99999 Notes: Assuming diploid individuals. Example: # See also http://samtools.github.io/bcftools/howtos/variant-calling.html bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf mpileup: option requires an argument -- 'h' Invalid option: '?' ----------------------------------------------