Variant Effect Predictor Line Count

[ashkot]

Hi all,
I am generating a VCF file and then running the Variant Effect Predictor (VEF) tool on it. This is in return giving me a new text file with the a list of variants and its potential effects. In one of the columns is the effect such as intronic change, exonic etc.

I wanted to get a line count for the total number of lines which have say for e.e exonic in a certain coulmn of the text file. Ideally, i would like to have a list of all variations and the number of lines for e.g.

Exonic = 200
Intronic = 600
...
...

If that's too complicated then i could simply have a single entity and run it multiple times.

Thanks in advance.
A

[Bukowski]

grep -v \# VEP_Annotation_File.ann | awk '{print $14}' | awk '{count[$1]++} END {for(j in count) print count[j], j}' | sort -nr

Works for me - but we have a modified VEP so I'm not sure the column name ($14) is the same in your case.

Output:

410 INTRONIC
277 DOWNSTREAM
138 UPSTREAM
119 3PRIME_UTR
99 WITHIN_NON_CODING_GENE,INTRONIC
51 INTERGENIC
46 NMD_TRANSCRIPT,INTRONIC
42 REGULATORY_REGION
28 WITHIN_NON_CODING_GENE
24 NON_SYNONYMOUS_CODING
15 5PRIME_UTR
9 SPLICE_SITE,INTRONIC
4 SYNONYMOUS_CODING
3 NMD_TRANSCRIPT,3PRIME_UTR
3 ESSENTIAL_SPLICE_SITE
2 NMD_TRANSCRIPT,SYNONYMOUS_CODING
2 CODING_UNKNOWN
1 STOP_GAINED
1 SPLICE_SITE,WITHIN_NON_CODING_GENE,INTRONIC

[ashkot]

worked

hi there,
thank you, thats awesome, it worked.

In one of the columns the chromosomal location is mentioned as 1:1000 (for e.g.), can this script be slightly tweaked such that i can get a list based for each chromosome, independant upon the consequence type.

For e.g.

chromosome 1 number of consequences
chromosome 2 number of consequences

thanks again.
a

[Bukowski]

You could just split your input file up into chromosomes and run it over each one couldn't you? It's all trivially achieved with a bit of shell scripting.