Galaxy |

Stacks2: gstacks (version 2.55+galaxy4)

Aligned data:

either the matches to the catalog (bam), i.e. tsv2bam, or reads aligned to a reference

Population map:

If set, matching will be done only for samples listed in this file

Mode:

Ignore paired-end reads:

ignore paired-end reads even if present in the input

Advanced options:

Model to use to call variants and genotypes:

Alpha threshold for discovering SNPs:

Default is 0.01 if the marukilow model is used (which is the case in refmap and denovomap), otherwise no default value is available.

Alpha threshold for calling genotypes:

Add log distribs output as dataset:

Add log output as dataset:

What it does

For de novo analyses, this program will pull in paired-end reads, if available, assemble the paired-end contig and merge it with the single-end locus, align reads to the locus, and call SNPs.

For reference-aligned analyses, this program will build loci from the single and/or paired-end reads before calling SNPs. The single- and paired-end reads must be aligned and stored together in the intput BAM or SAM files and the reads must be sorted. The gstacks program will detect if single- or paired-end reads are present.

In either mode, gstacks is able to remove PCR duplicates if requested.

Input files

If a population map is given BAM records must be assigned to samples using BAM "reads groups" (gstacks uses the ID/identifier and SM/sample name fields). Read groups must be consistent if repeated different files. Otherwise read groups are unneeded and ignored.

Output files

Assembled contigs and variant sites
Optional outputs: Read alignments and log.distribs

Created by:

Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko

Project links:

Stacks website

Stacks manual

Stacks google group