snp_store1

Main Options:

-o, --output OUTPUT_FILE

SNP output file (mandatory). Valid filetype is: .vcf.

-osc, --only-successful-candidates

Output only successfully called SNP candidates. Default: Output all candidates.

-dc, --dont-clip

Ignore clip tags in gff. Default: off.

-mu, --multi

Keep non-unique fragmentStore.alignedReadStore. Default: off.

-hq, --hide-qualities

Only show coverage (no qualities) in SNP output file. Default: off.

-sqo, --solexa-qual-offset

Base qualities are encoded as char value - 64 (instead of char - 33).

-id, --indel-file OUTPUT_FILE

Output file for called indels in gff format. Default: off. Valid filetype is: .gff.

-m, --method STRING

Set method used for SNP calling either threshold based or Maq method. One of thresh and maq. Default: maq.

-mp, --max-pile INTEGER

Maximal number of matches allowed to pile up at the same genome position. In range [1..inf]. Default: 1.

-mmp, --merged-max-pile

Do pile up correction on merged lanes. Default: off.

-mc, --min-coverage INTEGER

Minimal required number of reads covering a candidate position. In range [1..inf]. Default: 5.

-fc, --force-call INTEGER

Always call base if count is >= fc, ignore other parameters. Default: off. In range [1..inf]. Default: 10.

-oa, --orientation-aware

Distinguish between forward and reverse reads. Default: off.

-mpr, --max-polymer-run INTEGER

Discard indels in homopolymer runs longer than mpr. In range [0..inf]. Default: 100.

-dp, --diff-pos INTEGER

Minimal number of different read positions supporting the mutation. In range [0..inf]. Default: 0.

-eb, --exclude-border INTEGER

Exclude read positions within eb base pairs of read borders for SNV calling. Default: off. In range [0..inf]. Default: 0.

-su, --suboptimal

Keep suboptimal reads. Default: off

-re, --realign

Realign reads around indel candidates. Default: off

-pws, --parse-window-size INTEGER

Genomic window size for parsing reads (concerns memory consumption, choose smaller windows for higher coverage). In range [1..inf]. Default: 1000000.

Threshold method related:

-mm, --min-mutations INTEGER

Minimal number of observed mutations for mutation to be called. In range [1..inf]. Default: 3.

-pt, --perc-threshold DOUBLE

Minimal percentage of mutational base for mutation to be called. In range [0..inf]. Default: 0.25.

-mq, --min-quality DOUBLE

Minimal average quality of mutational base for mutation to be called. In range [0..inf]. Default: 10.

Maq method related:

-th, --theta DOUBLE

Dependency coefficient. In range [0..inf]. Default: 0.85.

-hr, --hetero-rate DOUBLE

Heterozygote rate. In range [0..1]. Default: 0.001.

-mmq, --min-map-quality INTEGER

Minimum base call (mapping) quality for a match to be considered. In range [0..inf]. Default: 1.

-ch, --corrected-het

Use amplification bias corrected distribution for heterozygotes. Default: off.

-maf, --mean-alleleFreq DOUBLE

Mean ref allele frequency in heterozygotes. In range [0..inf]. Default: 0.51.

-ac, --amp-cycles INTEGER

Number of amplification cycles. In range [0..inf]. Default: 18.

-ae, --amp-efficiency DOUBLE

Polymerase efficiency, probability of amplification. In range [0..1]. Default: 0.3.

-in, --initial-N INTEGER

Initial allele population size. In range [0..inf]. Default: 10.

-mec, --min-explained-column DOUBLE

Minimum fraction of alignment column reads explained by genotype call. In range [0..1]. Default: 0.8.

Indel calling options:

-it, --indel-threshold INTEGER

Minimal number of indel-supporting reads required for indel calling. In range [1..inf]. Default: 3.

-ipt, --indel-perc-threshold DOUBLE

Minimal ratio of indel-supporting/covering reads for indel to be called. In range [0..1]. Default: 0.25.

-iqt, --indel-quality-thresh INTEGER

Minimal average quality of inserted base/deletion-neighboring bases for indel to be called. In range [0..inf]. Default: 1.

-bsi, --both-strands-indel

Both strands need to be observed for indel to be called. Default: off.

-ebi, --exclude-border-indel INTEGER

Same as option -eb but for indel candidates. In range [0..inf]. Default: 0.

Other options:

-lf, --log-file STRING

Write log to FILE.

-v, --verbose

Enable verbose output.

-vv, --very-verbose

Enable very verbose output.

-q, --quiet

Set verbosity to a minimum.