Per Base Error Rate for Next-Gen Sequencing

[BertieWooster]

Hiya,

Given an alignment coverage table data (for Next-Gen), how would one go about computing the per base error rate?

Thx,
Bertie

[zslee]

samtools -pileup can produce base mapping and mutation information, does this help you ?

[nilshomer]

Hiya,

Given an alignment coverage table data (for Next-Gen), how would one go about computing the per base error rate?

Thx,
Bertie

Do you have the alignments in SAM/BAM format? If so, you can use the "dbamerrordist" program found in the DNAA package.