Hi,
I used Raindance technolofy to entich the exome of chromoxome X. Raindance uses PCR in nanodrops for enrichment.
Then I sequenced using HiSeq.
I want to know which of my targets were covered by at least 10 reads, for exmaple, and which targets are not covered.
I tried to use Picard CollectTargetedPcrMetrics , but got unreasonable results.
What I did:
got BAM files from Eland (from the NGS supplier).
Convereted to picard sorted bam files by SortSam
and then used CollectTargetedPcrMetrics, with the interval files from raindance:
AMPLICON_INTERVALS= primers list
TARGET_INTERVALS= targets list
Does anyone know what I did wrong?
I there an alternative free software for this analysis?
Picard CalculateHsMetrics always worked great for me in whole exome, and I cannot get any help or support from RainDance.
I will be grateful for any advice!
Thanks
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