------ Forwarded Message From: Kyle Chang <[email protected]> Date: Tue, 17 Apr 2012 15:55:51 -0500 To: Vanessa Kirkup Swing <[email protected]> Cc: <[email protected]>, Nipun Kakkar <[email protected]> Conversation: [Genome] How are ucsc dbsnp indel positions reported Subject: Re: [Genome] How are ucsc dbsnp indel positions reported
Right I understand that the positions are all 0-based, and I need to add 1 to get the same start coordinate as the genome browser. What I want to know is 1) if start position is actually the 1st deleted base or the base before the 1st deleted base of the deletion event. 2) In the case of insertion, is start position is 1bp before the actual insertion event. Kyle On 4/17/12 3:48 PM, "Vanessa Kirkup Swing" <[email protected]> wrote: Hi Kyle, Please see this FAQ on our coordinate system: http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1 I hope that clarifies things for you. If you have further questions, please email the list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Chang, Kyle <[email protected]> Date: Tue, Apr 17, 2012 at 10:02 AM Subject: [Genome] How are ucsc dbsnp indel positions reported To: "[email protected]" <[email protected]> Cc: "Kakkar, Nipun" <[email protected]> Hi, I have a question on how indel coordinates are reported in dbsnp tables. Here is a deletion record in dbsnp 135. Is 'start' always the 1st deleted base or is it like the vcf format which the start is always 1bp before 1st deleted base? E.g. 131 chr1 61341695 61341699 rs146746778 0 + TTTA TTTA -/TTTA genomic deletion Fo insertion, is 'start' reported as 1bp before insertion? So in this case, I imagine there's a CA insertion between 92536832 92536833 in 0-base coordinates. E.g. 161 chr1 92536832 92536832 rs72159935 0 + - - -/CA genomic insertion Best, Kyle _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome ------ End of Forwarded Message _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
