semvec/pypi-packages huggingface dataset:
sufam 0.4.2
So U Found A Mutation?
License: MIT
Keywords: Python validation mutation mpileup samtools pileup vcf bam

So U Found A Mutation? (SUFAM)
==============================
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    :target: http://anaconda.org/inodb/sufam
.. image:: https://travis-ci.org/inodb/sufam.svg?branch=master
    :target: https://travis-ci.org/inodb/sufam

Found a mutation in one or more samples? Now you want to check if they are in
another sample. Unfortunately mutect, varscan or whatever other variant caller
is not calling them. Use SUFAM. The super sensitive validation caller that
calls everything on a given position. All you need is a vcf with the mutations
that you are interested in and the sam/bam file of the sample where you want to
find the same inconsipicuous mutation.

Installation
------------
::

    pip install sufam

Run
---
::

    usage: sufam [-h] [--sample_name SAMPLE_NAME] [--format {matrix,sufam}]
                [--mpileup-parameters MPILEUP_PARAMETERS] [--version]
                reffa vcf bam

    So U Found A Mutation? (SUFAM)

    Found a mutation in one or more samples? Now you want to check if they are in
    another sample. Unfortunately mutect, varscan or whatever other variant caller
    is not calling them. Use SUFAM. The super sensitive validation caller that
    calls everything on a given position. All you need is a vcf with the mutations
    that you are interested in and the sam/bam file of the sample where you want to
    find the same inconsipicuous mutation.

    Author: inodb

    positional arguments:
    reffa                 Reference genome (fasta)
    vcf                   VCF with mutations to be validated
    bam                   BAM to find mutations in

    optional arguments:
    -h, --help            show this help message and exit
    --sample_name SAMPLE_NAME
                            Set name of sample, used in output [name of bam].
    --format {matrix,sufam}
                            Set output format [sufam]
    --mpileup-parameters MPILEUP_PARAMETERS
                            Set options for mpileup [--ignore-RG --min-MQ 1 --max-
                            depth 250000 --max-idepth 250000]
    --version             show program's version number and exit

Example
~~~~~~~
VCF file like::

    #CHROM	POS	ID	REF	ALT
    17	7574012	COSM11286,COSM214290	C	G
    17	7574012	COSM11286,COSM214290	C	A

Check if given mutations are in a bam file::

    sufam human_g1k_v37_chr17.fa mutations.vcf subset1.bam 2> example/sufam.log > example/sufam.tsv

Output:

- `example/sufam.log <example/sufam.log>`_
- `example/sufam.tsv <example/sufam.tsv>`_
 
Developers
----------
Tests
~~~~~
In root dir run::

    nosetests

For individual tests::

    nosetests -s tests/test_validation.py:TestValidation.test_validate_mutations_indel