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gsvar_format.md

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megSAP - GSvar format

In addition to the standard VCF format, megSAP creates variant lists in GSvar format in most analysis pipelines.

The GSvar format is a tab-separated text format which can be opened and filtered for example in Excel.

Variant filtering

There are several ways to filter variant lists in GSvar format to identify rare pathogenic variants:

  1. The file can be filtered in Microsoft Excel.
  2. The file can be filtered on the Linux command line using the VariantFilterAnnotations tool of ngs-bits.
  3. The file can be filtered interactively on Windows using the GSvar tool if ngs-bits (more documentation on GSvar coming soon).

Format details

Meta data header lines

Similar to VCF format, the GSvar format can contain meta data in header lines that start with ##:

  • The ##ANALYSISTYPE= header specifies the analysis type. It can be present only once. Valid analysis types are:
    GERMLINE_SINGLESAMPLE, GERMLINE_MULTISAMPLE, GERMLINE_TRIO, SOMATIC_SINGLESAMPLE, SOMATIC_PAIR

  • The ##SAMPLE= header specifies the analyzed sample name(s) and can contain additional annotations. It can be present several times.

  • The ##DESCRIPTION= header describes columns. It can be present several times.

  • The ##FILTER= header describes entries in the filter column. It can be present several times.

Main header line and variant lines

After the meta data header line, the main header line and the variant lines follow:

#chr	start	end	ref	obs	genotype	filter	quality	gene	variant_type	coding_and_splicing	RepeatMasker	dbSNP	1000g	ExAC	ExAC_hom	Kaviar	phyloP	Sift	MetaLR	PolyPhen2	FATHMM	CADD	OMIM	ClinVar	HGMD	COSMIC	ihdb_allsys_hom	ihdb_allsys_het	classification	classification_comment	validated	comment	gene_info
chr1	27682481	27682481	G	A	het	off-target	QUAL=2181;DP=169;AF=0.51;MQM=60	MAP3K6	intron	MAP3K6:NM_004672.4:intron:MODIFIER:exon27/28:c.3711+36C>T:,MAP3K6:NM_001297609.1:intron:MODIFIER:exon26/27:c.3687+36C>T:		rs12569127	0.1903	0.2656	4554/3529/231	0.2588											95	396					MAP3K6 (inh=n/a pLI=0.00)
...

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