view vt_decompose.xml @ 0:26babe3a66f1 draft default tip

planemo upload for repository https://github.com/atks/vt commit d4f5de5f229f503deb66a708f864cf380c900ce0

<tool id="vt_@BINARY@" name="VT @BINARY@" version="@VERSION@.0">
    <description>decomposes multiallelic variants into biallelic ones</description>
    <macros>
        <import>vt_macros.xml</import>
        <token name="@BINARY@">decompose</token>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <expand macro="version_command" />
    <command>
<![CDATA[

        ln -s "${ infile }" infile.vcf &&


        vt @BINARY@
            #if str($output_format) == 'bcf':
                -o decompose.bcf
            #else:
                -o decompose.vcf
            #end if
            $s
            infile.vcf

        &&
        ## For some reason, the file move will randomly produce empty files.
        ## Wait two seconds to let the system close file handlers and clean up.
        sleep 2
        &&

        #if str($output_format) == 'bcf':
            mv decompose.bcf "${ outfile }";
        #else:
            mv decompose.vcf "${ outfile }";
        #end if

]]>
    </command>
    <inputs>
        <param name="infile" type="data" format="vcf" label="VCF file to be normalised" />

        <param argument="-s" type="boolean" truevalue="-s" falsevalue=""
            selected="false" label="Smart decomposition"
            help="Splits up INFO and GENOTYPE fields that have number counts of R and A appropriately."/>

        <param name="output_format" type="select" label="Choose the output format" help="">
            <option value="bcf">BCF</option>
            <option value="vcf" selected="true">VCF</option>
        </param>
    </inputs>
    <outputs>
        <data name="outfile" format="vcf" label="${tool.name} on ${on_string}">
            <change_format>
                <when input="output_format" value="bcf" format="bcf" />
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="infile01.vcf" />
            <output name="outfile" file="decompose_result01.vcf" ftype="vcf" />
        </test>
        <test>
            <param name="infile" value="infile02.vcf" />
            <param name="s" value="True" />
            <output name="outfile" file="decompose_result02.vcf" ftype="vcf" />
        </test>
    </tests>
    <help>
<![CDATA[

**What it does**

Decompose multiallelic variants in a VCF file.
If the VCF file has genotype fields GT,PL, GL or DP, they are modified to reflect the change in alleles.
All other genotype fields are removed. The -s option will retain the fields and decompose fields of counts R and A accordingingly.

Decomposition and combining variants is a complex operation where the correctness is dependent on:

    * whether the observed variants are seen in the same sample
    * if same sample, whether they are homozygous or heterozygous
    * if both heterozygous, whether they are in the same haplotype or not (if known)

and one should be aware of the issues in handling variants resulting from such operations.
The original purpose of this tool is to allow for allelic comparisons between call sets. 

Standard option:

Before decomposition

.. code::

  #CHROM  POS     ID   REF     ALT         QUAL   FILTER  INFO                  FORMAT    S1                                     S2
  1       3759889 .    TA      TAA,TAAA,T  .      PASS    AF=0.342,0.173,0.037	GT:DP:PL	  1/2:81:281,5,9,58,0,115,338,46,116,809	 0/0:86:0,30,323,31,365,483,38,291,325,567

After decomposition

.. code::

  #CHROM  POS     ID   REF     ALT         QUAL   FILTER  INFO                                        FORMAT   S1               S2
  1	  3759889 .    TA      TAA	   .	  PASS    OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T    GT:PL    1/.:281,5,9      0/0:0,30,323
  1	  3759889 .    TA      TAAA        .      .       OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T    GT:PL    ./1:281,58,115   0/0:0,31,483
  1	  3759889 .    TA      T           .      .       OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T    GT:PL    ./.:281,338,809  0/0:0,38,567


One might want to post process the partial genotypes like 1/. to the best guess genotype based on the PL values.


With **-s** option:

Before decomposition

.. code::

  #CHROM  POS     ID   REF     ALT         QUAL   FILTER  INFO                  FORMAT    S1                                     S2
  1       3759889 .    TA      TAA,TAAA,T  .      PASS    AF=0.342,0.173,0.037	GT:DP:PL	  1/2:81:281,5,9,58,0,115,338,46,116,809	 0/0:86:0,30,323,31,365,483,38,291,325,567

After decomposition

.. code::

  #CHROM  POS     ID   REF     ALT         QUAL   FILTER  INFO                                                 FORMAT   S1               S2
  1	  3759889 .    TA      TAA	   .	  PASS    AF=0.342;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T    GT:PL    1/.:281,5,9      0/0:0,30,323
  1	  3759889 .    TA      TAAA        .      .       AF=0.173;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T    GT:PL    ./1:281,58,115   0/0:0,31,483
  1	  3759889 .    TA      T           .      .       AF=0.037;OLD_MULTIALLELIC=1:3759889:TA/TAA/TAAA/T    GT:PL    ./.:281,338,809  0/0:0,38,567

In general, you should recompute fields that involves alleles after decomposition.  Information is generally lost after vertically decomposing a variant, so care should be taken in interpreting the resultant values.

@CITATION@
]]>
    </help>
    <expand macro="citations"/>
</tool>