How to filter SNP in usegalaxy

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1

How to filter SNP in file (A)as region in defined range in file (B) in usegalaxy?
A:
chr1 186 187 rs378896312
chr1 703 704 rs136740087
chr1 833 834 rs136710007
chr1 864 865 rs43096727
chr1 1610 1611 rs132965558
chr1 1611 1612 rs134909289
chr1 1628 1629 rs136933083

B:
chr1 185 190
chr1 800 840
chr1 1600 1620
chr1 1625 1630

output:
chr1 186 187 rs378896312
chr1 833 834 rs136710007
chr1 1610 1611 rs132965558
chr1 1611 1612 rs134909289
chr1 1628 1629 rs136933083

2

I hope I understand your question correctly. You want to have the SNPs in file A that are to 100% in the ranges listed in your file B, and thus generating your desired output?

The tool you are searching for is bedtools Intersect intervals. Make sure to tick the option: Write the original A entry once if any overlaps found in B. and under Required overlap that you give Minimum overlap required as a fraction of A the value 1.0.

A detailed explaination of the tool is given in Galaxy and here.