所以你发现了突变？
sufam的Python项目详细描述
在一个或多个样本中发现突变？现在你想看看他们是否在 另一个样本。不幸的是，mutect、varscan或其他变量调用程序 不是给他们打电话。使用苏法姆。超级敏感的验证调用程序 把所有东西都放在一个特定的位置上。你只需要一个有突变的VCF 你感兴趣的和你想要的样本的sam/bam文件 找到同样的无关紧要的突变。
安装
pip install sufam
运行
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
示例
VCF文件，如：
#CHROM POS ID REF ALT 17 7574012 COSM11286,COSM214290 C G 17 7574012 COSM11286,COSM214290 C A
检查给定的突变是否在BAM文件中：
sufam human_g1k_v37_chr17.fa mutations.vcf subset1.bam 2> example/sufam.log > example/sufam.tsv
输出：
开发人员
测试
在根目录下运行：
nosetests
对于个别测试：
nosetests -s tests/test_validation.py:TestValidation.test_validate_mutations_indel
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