1% VCFSAMPLEDIFF(1) vcfsamplediff (vcflib) | vcfsamplediff (VCF transformation)
2% Erik Garrison and vcflib contributors
3
4# NAME
5
6**vcfsamplediff**
7
8# SYNOPSIS
9
10**vcfsamplediff** [options] <tag> <sample> <sample> [ <sample> ... ] <vcf file>
11
12# DESCRIPTION
13
14Establish putative somatic variants using reported differences between germline and somatic samples. Tags each record where the listed sample genotypes differ with <tag>. The first sample is assumed to be germline, the second somatic. Each record is tagged with <tag>={germline,somatic,loh} to specify the type of variant given the genotype difference between the two samples.
15
16
17
18# OPTIONS
19
20```
21
22
23options:
24    -s --strict     Require that no observations in the germline support the somatic alternate.
25
26
27Type: transformation
28
29```
30
31
32
33
34
35# EXIT VALUES
36
37**0**
38: Success
39
40**not 0**
41: Failure
42
43# SEE ALSO
44
45
46
47[vcflib](./vcflib.md)(1)
48
49
50
51# OTHER
52
53## Source code
54
55[vcfsamplediff.cpp](https://github.com/vcflib/vcflib/blob/master/src/vcfsamplediff.cpp)
56
57# LICENSE
58
59Copyright 2011-2020 (C) Erik Garrison and vcflib contributors. MIT licensed.
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