Hello,
I have used the GATKv3.0 pipeline to align and call variants on whole exome data. Recently, i was asked to get the variants from raw data sequenced using ION PGM. The data I get have been obtained by sequencing around a list of hundreds of variants. It means that i get a pretty small fastq file.
I know that using -L option it is possible to call variants around specific intervals (it save hours). My question is :
Is there a non-commercial tool that enables to fasten the alignment process by looking just around targetted intervals on my reference genome.
eg. for bwa, something like:
thanks
colin
I have used the GATKv3.0 pipeline to align and call variants on whole exome data. Recently, i was asked to get the variants from raw data sequenced using ION PGM. The data I get have been obtained by sequencing around a list of hundreds of variants. It means that i get a pretty small fastq file.
I know that using -L option it is possible to call variants around specific intervals (it save hours). My question is :
Is there a non-commercial tool that enables to fasten the alignment process by looking just around targetted intervals on my reference genome.
eg. for bwa, something like:
Code:
bwa bwasw hg19ref.fa [COLOR="DarkGreen"]-L intervals.bed[/COLOR] mysample.fastq
colin
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