[B]Mpileup on multiple BAM files, common SNPs?[/B]

[hbt]

Does anyone know the best way to discover only the common SNPs across multiple Bam files?
Is this best achieved running each Bam individually and somehow filtering the vcf files or can it be done by inputting all Bam files at the mpileup stage?

would be very grateful if anyone could share their commands/experience

many thanks

Huw

[hbt]

Anyone.........?

[swbarnes2]

You can import multiple .bams into mpileup.

[hbt]

You can import multiple .bams into mpileup.

Thank you, but how could I determine which SNPs in the resulting output file were unique to one of the input BAMs and which were common across all in-putted BAMs?

[pallevillesen]

Use:

bedtools intersect -a file1 -b file2 >overlap_1_2
bedtools intersect -a overlap_1_2 -b file3 >overlap_1_2_3

Works on any SNP caller outputting in vcf / bed format.