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Old 05-13-2019, 12:38 AM   #1
anu18
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Location: england, UK

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Default vcf file opening issues with a text editor

Hello,

I have created a vcf file which i can open using bcf tools in the terminal but not in the windows using a text editor. I can see the header information of the vcf file but the actual variant calls appear as symbols. Can someone help with this.
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Old 05-20-2019, 08:19 PM   #2
finswimmer
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You probably have a bcf file rather than a vcf.

You can use bcftools to convert it if needed.

Code:
bcftools view input.bcf > output.vcf
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Old 05-22-2019, 09:04 AM   #3
anu18
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Thanks. I have a new question now. I was trying to plot the variants stats using plot-vcfstats. i am getting this error. Kindly advise

Parsing bcftools stats output: diploidall.stats
Plotting graphs: python /rds/projects/2018/leachlj-atmeiosis/RAD_bham/diploids/merged/variants1/diplostats//plot.py
Traceback (most recent call last):
File "/diploids/merged/variants1/diplostats//plot.py", line 51, in <module>
import matplotlib as mpl
ImportError: No module named matplotlib
The command exited with non-zero status 256:
python /rds/projects/2018/leachlj-atmeiosis/RAD_bham/diploids/merged/variants1/diplostats//plot.py

at /rds/bear-apps/handbuilt/software/bcftools/v1.2_gcc-v4.7.2/bin/plot-vcfstats line 78.
main::error('The command exited with non-zero status 256:\x{a}\x{9}python /rds/pro...') called at /rds/bear-apps/handbuilt/software/bcftools/v1.2_gcc-v4.7.2/bin/plot-vcfstats line 271
main:lot('HASH(0x25d4020)') called at /rds/bear-apps/handbuilt/software/bcftools/v1.2_gcc-v4.7.2/bin/plot-vcfstats line 67
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