Stampy - Mapping multiple individuals to genome

[vivi7]

Stampy - Mapping multiple individuals to genome
Hi everybody,

I am very very new to this world, so apologize if the following questions are too basic...
I am trying to use Stampy to map my RAD-seq reads to a reference genome.
I have double digested, paired end data from multiple individuals of 6 species and the genome of one of those species.

I created the genome file and the hash table. According to the manual when mapping paired end data to a genome the script should look something like that:

./stampy.py -g hg18 -h hg18 -M solexareads_1.fastq solexareads_2.fastq

My questions are:

1) is it possible to map multiple individuals to the genome in one go or should I map each individual singularly to it? Could I use for example something like:
./stampy.py -g hg18 -h hg18 -M ind1_1.fastq ind1_2.fastq ind2_1.fastq ind2_2.fastq ind3_1.fastq ind3_2.fastq ?

2) which option can be added to specify the number of mismatches allowed between reads and genome? I didn't understand it from the help...

Any help would be greatly appreciated

Many many thanks
Vivi

[vivi7]

Hi again,

I am posting the reply I got from Gerton Lunter,
so that if someone new to the field like me will have same problems will find an answer hopefully

'1: no, you should map one sample in one go. If you want, you can merge the BAM files afterwards; if you want to do that, you should 'tag' each set of reads with a unique 'read group' identifier; the --help will tell you how to do this.

2. This is not possible, but also not necessary. Stampy will map reads if it finds a location in the genome that is more similar to the read than would be expected purely by chance for the best-matching locus in a fully random genome of this size -- up to some threshold that is implicitly set by the algorithm, and corresponds to ~10-15% divergence.

Hope this helps!
Best wishes

Gerton'