I am trying to sort a genetic file based on chr (column 2) and position (column 3) that both start from lower to higher. my table is like this in large file
SNP CHR BP A1 A2 effect_allele_frequency BETA standard_error P
rs10875231 1 100000012 T G 0.405 -0.0456807 0.02260471 0.04335677
rs6678176 1 100000827 C T 0.383 0.02553138 0.02287662 0.2645817
rs78590530 1 100000948 A G 0.016 0.171376 0.08757958 0.05035017
rs149636485 1 100001060 A G 0.004 -0.03363731 0.1819208 0.8529224
I want to order CHR (from 1 to 22) in a way that position also start from lower to high disregard of other columns and for each chr separately. I tried this sort command
sort -t $'\t' -nk3 myfile.tsv | sort -t $'\t' -nk2 > test.txt
it gives order in chr (column 2) but not position (column 3). it seems that column 1 interferes:
SNP CHR BP A1 A2 effect_allele_frequency BETA standard_error P
rs1000033 1 226580387 G T 0.416 0.02958699 0.02295015 0.1971771
rs1000050 1 162736463 T C 0.378 0.06136397 0.02293639 0.007468015
rs1000070 1 222359612 C T 0.381 0.02563547 0.02294139 0.2638107
rs1000073 1 157255396 G A 0.387 -0.01470793 0.02273634 0.517414
rs1000085 1 66857915 C G 0.024 -0.03536382 0.07555889 0.6394446
rs1000127 1 63432716 C T 0.157 0.003052272 0.03045933 0.919875
How can I sort by column 2 then 3 only?
