VCF using Python
2
0
Entering edit mode
4 days ago
V Vera • 0

I am looking for a python script to merge two vcf files into a single VCF file, so that overlapping variants are present only once in the output file

Python VCF • 188 views
ADD COMMENT
2
Entering edit mode
4 days ago

bcftools merge

ADD COMMENT
1
Entering edit mode
4 days ago
sbstevenlee ▴ 320

Check out the pyvcf.merge() method (documentation) and the pyvcf.VcfFrame.merge() method (documentation) in the Python package fuc (documentation). If you have any questions about the use of these methods, please feel free to leave a comment (I'm the author of fuc).

ADD COMMENT
0
Entering edit mode

Thankyou for your kind reply. The assignment says that avoid usage of Pandas or any other vcf reader modules to read vcf files. and Solve using core python data structures. I am pretty much newbie in this field and still trying to grasp the assignment.

ADD REPLY

Login before adding your answer.

Traffic: 2249 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6