# mnake sure all rows have 99 fields | |
$ awk 'BEGIN{FS="\t"} {print NF}' /uufs/chpc.utah.edu/common/home/u1072926/gemini_queries/all.txt | uniq | |
99 | |
# how many HET (1) and HOM_ALT (3) genotypes were there? | |
$ awk 'BEGIN{FS="\t"} {print $99}' /uufs/chpc.utah.edu/common/home/u1072926/gemini_queries/all.txt | sort | uniq -c | |
# get rid of headers except for the first one | |
(head -n 1 /uufs/chpc.utah.edu/common/home/u1072926/gemini_queries/all.txt; grep -v gt_types /uufs/chpc.utah.edu/common/home/u1072926/gemini_queries/all.txt) | |
# make sure there are no LOW entries (note grep -w for specifificty) | |
(head -n 1 /uufs/chpc.utah.edu/common/home/u1072926/gemini_queries/all.txt; grep -v gt_types /uufs/chpc.utah.edu/common/home/u1072926/gemini_queries/all.txt) | grep -w LOW | |
# what col number is the gene column? | |
head -1 /uufs/chpc.utah.edu/common/home/u1072926/gemini_queries/all.txt | tr "\t" "\n" | cat -n | grep gene | |
20 gene | |
# print, in descending order, the number of variants observed per gene | |
awk '{print $20}' /uufs/chpc.utah.edu/common/home/u1072926/gemini_queries/all.txt | sort | uniq -c | awk '{print $2"\t"$1}' | sort -k2,2nr | head -n 50 | |
MUC16 25126 | |
MUC6 20998 | |
AHNAK2 8647 | |
TTN 8244 | |
MUC5B 6907 | |
MUC19 6872 | |
FLG 6681 | |
NBPF10 6375 | |
ANKRD36 5687 | |
HRNR 5576 | |
NBPF1 5472 | |
FAM230A 4745 | |
PABPC3 4733 | |
FAM182B 4497 | |
FRG1B 4409 | |
PDE4DIP 4334 | |
TAS2R31 4208 | |
IGFN1 4176 | |
FCGBP 3925 | |
OBSCN 3869 | |
MUC2 3636 | |
AHNAK 3621 | |
TAS2R43 3586 | |
SERPINA1 3432 | |
CTD-3088G3.8 3371 | |
TAS2R19 3115 | |
ANKRD36C 3096 | |
MKI67 3073 | |
ANKRD30B 2986 | |
TAS2R46 2905 | |
NBPF14 2796 | |
GOLGA6L2 2717 | |
NEB 2652 | |
PRAMEF1 2621 | |
TCHH 2564 | |
FLG2 2548 | |
KRT18 2455 | |
ZNF257 2412 | |
NBPF12 2374 | |
PLIN4 2371 | |
NBPF9 2349 | |
FAM186A 2348 | |
PRAMEF2 2345 | |
PRAMEF4 2251 | |
OR4A16 2247 | |
GXYLT1 2228 | |
CNN2 2200 | |
FSIP2 2194 | |
RP11-683L23.1 2173 | |
LILRA6 2137 |
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