I have a multi-sample vcf file and I want to get a table of IDs on the left column with the variants in which they have an alternate allele in. It should look like this:
ID1 chr2:87432:A:T_0/1 chr10:43234:C:G_1/1
ID2 chr2:87432_A:T_1/1
ID3 chr11:432434:T:G chr14:34234234:C:G chr20:34324234:T:C
This is to then read into R
I have tried combinations of:
bcftools query -f '[%SAMPLE\t] %CHROM:%POS:%REF:%ALT[%GT]\n'
but I keep getting sample IDs overlapping on the same line and I can't quite figure out the sytnax.
Your help would be much appreciated
You cannot achieve what you want with a single BCFtools command. BCFtools parses one VCF variant at a time. However, you can use a command like this to extract what you want:
bcftools +split -i 'GT="0/1" | GT="1/1"' -Ob -o DIR input.vcf
This will create one small .bcf file for each sample and you can then run multiple instance of bcftools query to get what you want
I added a dummy column at the beginning of my data export to a CSV file to get rid of control characters and some specific string values as mentioned below by using a pipe '|' delimiter. This data is coming from Teradata fast export using utf-8
'''
y^CDUMMYCOLUMN|
<86>^ADUMMYCOLUMN|
<87>^ADUMMYCOLUMN|
<94>^ADUMMYCOLUMN|
{^ADUMMYCOLUMN|
_^ADUMMYCOLUMN|
y^CDUMMYCOLUMN|
[^ADUMMYCOLUMN|
k^ADUMMYCOLUMN|
m^ADUMMYCOLUMN|
<82>^ADUMMYCOLUMN|
c^ADUMMYCOLUMN|
<8e>^ADUMMYCOLUMN|
<85>^ADUMMYCOLUMN|
'''
This is completely random and not every row has these special characters. I'm sure I'm missing something here. I'm using sed to get rid of dummycolumn and control characters.
'''$ sed -e 's/.*DUMMYCOLUMN|//;/^$/d' data.csv > data_output.csv'''
After running this statement, I'm still remaining these below random values.
'''
<86>
<87>
<85>
<94>
<8a>
<85>
<8e>
'''
I could have written a sed statement to remove first three letters from each row but this series is not appearing in every row. At the same time, row count is 400 Million.
Current output.
y^CDUMMYCOLUMN|COLUMN1|COLUMN2|COLUMN3
<86>^ADUMMYCOLUMN|6218915846|36596|12
<87>^ADUMMYCOLUMN|9822354765|35325|33
t^ADUMMYCOLUMN|6788793999|111|12
g^ADUMMYCOLUMN|6090724004|7017|12
_^ADUMMYCOLUMN|IC-21357688806502|111|12
<8e>^ADUMMYCOLUMN|9682027117|35335|33
v^ADUMMYCOLUMN|6406807681|121|12
h^ADUMMYCOLUMN|6346768510|121|12
V^ADUMMYCOLUMN|6130452510|7017|12
Desired Output
COLUMN1|COLUMN2|COLUMN3
6218915846|36596|12
9822354765|35325|33
6788793999|111|12
6090724004|7017|12
IC-21357688806502|111|12
9682027117|35335|33
6406807681|121|12
6346768510|121|12
6130452510|7017|12
Please help.
Thank you.
I have a requirement to replace multiple columns of a csv file with its base64 encoding value which should be applied to some columns of the file but keep the first line unaffected as the first line contains the header of the file. I have tried out for 1 column as below but as I have given it to proceed after skipping the first line of the file it is not
gawk 'BEGIN { FS="|"; OFS="|" } NR >=2 { cmd="echo "$4" | base64 -w 0";cmd | getline x;close(cmd); print $1,$2,$3,x}' awktest
o/p:
12|A|B|Qw==
13|C|D|RQ==
36|Z|V|VQ==
Qs: It is not showing the header in the output. What should I do to make produce the header in the output? Also can I use any loop here to replace multiple columns?
input:
10|A|B|C|5|T|R
12|A|B|C|6|eee|ff
13|C|D|E|9|dr|xrdd
36|Z|V|U|7|xc|xd
Required output:
10|A|B|C|5|T|R
12|A|B|encodedvalue|6|encodedvalue|ff
13|C|D|encodedvalue|9|encodedvalue|xrdd
36|Z|V|encodedvalue|7|encodedvalue|xd
Is this possible? Have researched a lot but could not find a proper explanation. I am new to shell. Kindly help. Many thanks!!!!
It looks like you can just sequence conditionals. This may not be the best way of solving the header issue, but it's intuitive.
BEGIN { FS="|"; OFS="|" } NR ==1 {print} NR >=2 { cmd="echo "$4" | base64 -w 0";cmd | getline x;close(cmd); print $1,$2,$3,x}
As for using a loop to affect multiple columns... Loops in bash are hard. Awk is technically its own language, and may have a looping construct of it's own, IDK. But it's not clear you need a loop. If there's only a reasonable number of fields that need modifying, you can just parameterize the existing command (somehow) by the field index, and then pipe through however many instances of it. It won't be as performant as doing it all in a single pass of awk, but that's probably ok.
I have an existing perl one-liner (from the Edwards lab) that works wonderfully to read a text file (named ids.file) that contains one column of IDs and searches a second, specially formatted text file (named fasta.file in this example - in "fasta" format for those who know bioinformatics) and returns sequences that match the ID from the first file. I was hoping to expand this script to do two additional things:
The current perl one-liner only seems to work if the ids.file contains one column of data. I would like it to work on a file that contains two columns (separated by spaces), and act on the second column of data (well, really any column of data, but I assume that it will be obvious enough to adapt it if someone can give an example using a second column)
I would like to append the any results returned from the output of the search to a third column, instead of just to a new file.
If someone is kind enough to offer an example but only has time or inclination to work on one of these, I would prefer that you try to solve #2 - I have come close to solving #1 with a for loop that uses awk to only use the Perl code on the second column - I haven't gotten it yet, but am close, so #2 seems like the harder one to me.
The perl one liner is as follows:
perl -ne 'if(/^>(\S+)/){$c=$i{$1}}$c?print:chomp;$i{$_}=1 if #ARGV' ids.file fasta.file
I appreciate any help you can give!
Not quite sure but will this do?
perl -ne 'chomp; s/^>(\S+).*/$c=$i{$1}/e; print if $c;
$i{(/^\S*\s(\S*)$/)[0]}="$_ " if #ARGV'
ids.file fasta.file
I have a CSV file containing some user data it looks like this:
"10333","","an.10","Kenyata","","Aaron","","","","","","","","","",""
"12222","","an.4","Wendy","","Aaron","","","","","","","","","",""
"14343","","aaron.5","Nanci","","Aaron","","","","","","","","","",""
I also have a file which has an item on each line like this:
an.10
arron.5
What I want is to find only the lines in the CSV file contained in the list file.
So desired output would be:
"10333","","an.10","Kenyata","","Aaron","","","","","","","","","",""
"14343","","aaron.5","Nanci","","Aaron","","","","","","","","","",""
(Note how an.4 is not contained in this new list.)
I have any environment available to me and am willing to try just about anything aside from manually doing so as this csv contains millions of records and there are about 100k entries in the list itself.
How unique are the identifiers an.10 and the like?
Maybe a very small *x shell script would be enough:
for i in $(uniq list.txt); do grep "\"$i\"" data.csv; done
That would, for every unique entry in the list, return all matching lines in the csv file. It does not match exclusively on the second column however. (That could be done with awk for example)
If the csv file is data.csv and the list file is list.txt, I would do this:
for i in `cat list.txt`; do grep $i data.csv; done