Question of retrieving nucleotides from a list of genomic coordinates..

[westerman]

Since a BAM should contain overlapping reads that may or may not agree at any particular base instead of a single sequence then the answer to your question is not straight-forward. First you'll need to generate a consensus sequence via 'samtools', 'bcftools' and 'vcfutils' ... see: http://samtools.sourceforge.net/mpileup.shtml. Having gotten that then you can pull out the bases.

There may be easier ways but that is how I would do it.

[shyam_la]

It's trivial to convert a sorted BAM file into a bed file.
Look at bedtools documentation. (bamtobed, in particular)

No I meant a BAM file in place of a fasta file..

[jparsons]

It's trivial to convert a sorted BAM file into a bed file.
Look at bedtools documentation. (bamtobed, in particular)

[shyam_la]

Thank you. Will try that out.. Is it possible to do a similar thing with an aligned sorted BAM file?

[dariober]

Lets say I have an excel file, one column with chr number and the next with genomic coordinates, running into several thousands in numbers. Is there some online / offline tool into which I can input this information and get as output the nucleotides at these loci in hg19?

For eg.
Input
1 23354
2 345344
3 43543553

Output
1 23354 T
2 345344 C
3 43543553 A

If could reformat your excel file to BED format (even within excel) and save it as plain text (say as mypositions.bed). Then, you can use bedtools as something like (assuming you have already the FASTA file for hg19):

bedtools getfasta -fi hg19.fa -bed mypositions.bed -tab

Dario

[shyam_la]

Lets say I have an excel file, one column with chr number and the next with genomic coordinates, running into several thousands in numbers. Is there some online / offline tool into which I can input this information and get as output the nucleotides at these loci in hg19?

For eg.
Input
1 23354
2 345344
3 43543553

Output
1 23354 T
2 345344 C
3 43543553 A