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10XGenomics / longranger

10x Genomics Linked-Read Alignment, Variant Calling, Phasing, and Structural Variant Calling
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Longranger alignment statisitcs #5

Open nadiabeyg opened 4 years ago

nadiabeyg commented 4 years ago

Dear all, I am using longranger align for mapping tetraploid plant samples (10x reads) (Potato-tetraploid) on my reference. Overall alignment rate is 95%. For variant calling i am interested in choosing properly paired end reads and in my case its too low (67.35%). Why longranger reports low properly paired end reads and whats the mechanism /algorithm behind reporting these reads)? Is there any other better option for aligning 10x linked reads? Secondly longranger wgs works for tetraploid samples as well? Because I normaly use freebayes separately to call variants across all samples as I have both diploid and tetraploid samples.

pmarks commented 4 years ago

Hi Nadia, Please write in to our support team at support@10xgenomics.com for assistance. Thanks!