Hi everyone, I am working with some SNPs analisys/filtering and came across with a challeging task. After filtering for the alterations of interest, I got a file with the follwoing configuration:
01_126729_C
01_85829_G
02_11867_A
02_171665_C
02_183470_A,T
03_225197_G
03_360822_T
03_364428_T
03_51665_C
03_66720_A
In which 01_, 02_, ... represent chromosomes. I need to split this single column into multiple columns, containing only the SNPs from one chromossome per column. I don have a clue on how to do this! Could anyone please help me with this? That would save me a lot of boring work on excel!
Cheers!
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written
by
jezielbqi •
2 answers
First split on "_" and the sort on the "chromosome" column. Both can be done in many different ways - including Excel, R and command line (google). In Excel, the splitting function is inside the "DAta" tab, and is named as "Text to Columns".
Here's a multi-step process so you can see how it's done:
Pull out the chromosome ids from your file
cut -f 1 -d '_' infile.txt | sort | uniq > all_chrom_ids.txt
Put this into a bash file (get_ids.sh):
#!/usr/bin/bash
grep -e "$1"_ all_chrom_ids.txt > "$1"_snps.txt
Use your ids to make a file, one for each chromosome, containing the snps for that chromosome:
cat all_chrom_ids.txt | xargs -n 1 bash get_ids.sh
Paste each file by tab:
paste *_snps.txt > snps_by_chrom_col.txt
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