First, for numbers that have two commas, remove two commas within the quotes.
Second, for numbers that have only 1 comma, remove one comma within the quotes.
Finally, remove quotes.
sed -e 's/\(".*\),\(.*\),\(.*"\)/\1\2\3/g' tableofSNPs.csv | sed -e 's/\(".*\),\(.*"\)/\1\2/g' | sed 's/\"//g' > tableofSNPs_changed.csv
Output check
It showed three commas(",,,") which means it worked.
sed -e 's/[^,]//g' tableofSNPs_changed.csv | uniq
### Extra task: A to T, T to A
If we change A to T directly and then change T to A, all original A will remain A. So, we need to change A to another character except T, then convert T to A. At last, convert those symbols to T.
sed -E 's/A/!/g' tableofSNPs.csv | sed -E 's/T/A/g' | sed -E 's/!/T/g' > tableofSNPs_recover.csv
@cecileane @coraallencoleman
Change data format
Output check
sed -E 's/A/!/g' tableofSNPs.csv | sed -E 's/T/A/g' | sed -E 's/!/T/g' > tableofSNPs_recover.csv