Thanks Ram. I re-check the vcf.file with grep -c -v "^#", it gives me the same number (73,592). Yes, the first line of matrix.012 is a sample GT column. Actually, I use head -n 5 matrix.012 | awk -F "\t" '{print NF}', it gives me the same number (73,593) for all 5 lines. Confusing...
vcf to SNPmatrix through vcftools --012 produces extra column
Hello all,
I am using vcftools to produce a SNPmatrix from vcf file for eQTL analysis, the vcf file contain 73,592 SNPs (grep -c -v "#" vcf.file).
However, after (vcftools --vcf vcf.file --012 --out matrix), I got three separate files --- matrix.012.indv, matrix.012.pos, matrix.012. However, when I check the column number of matrix.012 through (head -n 1 matrix.012 | awk '{print NF}'), it gives me 73,593, which is 1 more than the actual SNPs number. Weird thing is the row number of matrix.012.pos (wc -l matrix.012.pos) is 73,592. Any suggestions about how I could fix this?
Thanks a lot.
1 answer
Ensure you're only excluding header lines, not variant records that contain a #: grep -vc "^#" vcf.file. Also, try specifying the separator explicitly for awk in your NF calculation.
Did you look at the first column in matrix.012 and make sure it's a sample GT column? I think it may be a metadata or some such column.
Try
head matrix.012 | cut -f1-10 | column -ts $'\t' | less -S
head matrix.012 | cut -f 73585-73593 | column -ts $'\t' | less -S
Maybe the last column is blank. Also try
head -n 1 matrix.012 | tr "\t" "\n" | head -n 100 | cat -te | less -SN
head -n 1 matrix.012 | tr "\t" "\n" | tail -n 100 | cat -te | less -SN
No problem, the metadata nature was difficult to spot as they're all numbers. My commands did the following:
- The first set picked the first and last few columns of the first 10 rows and pretty-printed them so columns would line up regardless of "cell" content length
- The second set picked the first and last 100 columns in the first row and transposed the vector to vertical (tabs -> new lines) and then printed all characters including invisibles. This would show us if there were a trailing empty column owing to lines ending in a delimiter character.
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