10000 GitHub - TuBieJun/strtk: a tool to deal with wegene string format genotype data.
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a tool to deal with wegene string format genotype data.

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TuBieJun/strtk

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strtk： 处理str seq数据的工具

strtk由多个模块组成。

view

查看指定区间或位点或染色体的genotype

strtk view -s in_str_file -i index_file -r 1:1-10000
strtk view -s in_str_file -i index_file -r 1:10000
strtk view -s in_str_file -i index_file -r X

stats

统计str 数据的位点个数、杂合率和call rate。可以选择指定区间

strtk stats -s in_str_file
strtk stats -s in_str_file -r 1:1-10000

com

比较两个str seq的一致性。 可以选择指定区间，是否过滤indel。

strtk com -s1 in_str_file1 -s2 in_str_file2
strtk com -s1 in_str_file1 -s2 in_str_file2 -i index_file -r X -f #只比较X染色体的snp位点

str2vcf

将str file转为vcf格式。 可以选择指定区间， 是否过滤no call和indel。

strtk str2vcf -s in_str_file -f -n -i index_file -o out.vcf -I sampleid -r X:1-10000

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a tool to deal with wegene string format genotype data.

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