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Old 03-21-2017, 02:50 AM   #1
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Default snpeff software

dear all
i have problem in building the database manually in snpeff database
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Old 03-21-2017, 03:19 AM   #2
GenoMax
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You need to provide additional information before people can help.

What command are you running? What error do you get (if any)?
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Old 03-31-2017, 11:19 PM   #3
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Default SNPeff database building error

java.lang.RuntimeException: FATAL ERROR: Most Exons do not have sequences!
There might be differences in the chromosome names used in the genes file ('/home/crpgws2/Desktop/snpEff/./data/ver6/genes.gff')
and the chromosme names used in the 'reference sequence' file.
Please check that chromosome names in both files match.

I got this error while running the snpeff database building command. Should I modify my chromosome name in ref seq or I have to modify the gff file. I am doing this to create Vigna radiata reference. Please let me know what can i do to solve this problem.
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Old 04-02-2017, 05:10 PM   #4
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For reference cross-posted: https://www.biostars.org/p/245158

Can you answer the questions there?
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Old 04-05-2017, 01:49 AM   #5
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I have run SNPeff successfully. but i found some problem in html output file, as my input VCF line number and variants before filter are two different numbers. While in my view that must be same. What can be the reason for this variation although In my Input vcf and output vcf have the same no. of entries, but still the html stats varies from this number.


Summary
Genome ver6
Date 2017-04-05 11:58
SnpEff version
SnpEff 4.3k (build 2017-03-29 17:16), by Pablo Cingolani
Command line arguments
SnpEff ver6 VIGNA_SUBLOBATA_SNV.vcf
Warnings 70,058
Errors 0
Number of lines (input file) 100,273
Number of variants (before filter) 104,184
Number of not variants
(i.e. reference equals alternative) 0
Number of variants processed
(i.e. after filter and non-variants) 103,341
Number of known variants
(i.e. non-empty ID) 0 ( 0% )
Number of multi-allelic VCF entries
(i.e. more than two alleles) 1,382
Number of effects 223,468
Genome total length 463,637,892
Genome effective length 333,860,997
Variant rate 1 variant every 3,230 bases
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