![]() ![]() CLAN LORD RANGER STUDIES MANUALI have zero MAPQ reads toggled off in IGV so didn't see that on the initial manual inspection. The variant calling scored 100% although FGC5865 was called as 0/1 due to the inclusion of 8 MAPQ=0 reads. The mapping to hg38 has been done using minimap2 as with the Dante long read data and SNPs called as before with varscan. CLAN LORD RANGER STUDIES DOWNLOADThere were also links to download the paired end FASTQ files but the files were not accessible so I extracted them from the BAM using Picard for local realignment. ![]() This should serve as a warning to anyone being told by *any* vendor that you don't need a BAM file! Without the actual data you are at the mercy of the arbitary variant calling protocols of the lab. Two FGC novel variants that were not previously called in the Dante VCF - FGC5870 and FGC5873 - were confirmed as derived in the raw data. The BAM file for my Dante short read WGS has now been delivered online and was downloaded yesterday and forwarded to. The evaluation of the marketplace continues with pilot test data now in from both Chronomics and Sano Genetics. Another test has just been kicked off at the lab. The default threshold in varscan is 8 reads and this position only got 5.ġ2.2.20 Last year was a very successful one for the project with 30 male Kennedys being DNA sequenced and uploaded to the Kennedy project tree at YFull. As of autumn 2020 they are only offering short read tests but I remain hopeful they will re-enter the nanopore market in due course.Ģ.3.20 Updated the varscan spreadsheet with my Sano Genetics BAM file analysis, this scored 16/17 on the FGC NVs just missing FGC5856 due to insufficient depth. In addition all data inluding a BAM file of the entire genome are immediately available for download with the reports - some companies charge you extra for the raw data and don't even reveal the fee at the time you order the actual test! The new Italian startup Dante Labs continue their activities but sadly their customer service remains erratic, although they have offered both short and long read nanopore tests previously. It is head and shoulders above all the others in terms of quality, turnaround and the scope of the analysis reports. Out of these, the WGS (whole genome) test remains the flagship product and the mainstay of the Kennedy DNA project. The total number of labs utilised is sixteeen! It is doubtful anyone else has carried out such a breadth of testing across the market and maintains a commitment to continue doing so as new options arise. ![]() In addition I have also carried out six different SNP array/'chip' tests as well as used microsatellite (legacy STR) tests from six different vendors. Ayrshire and Perthshire especially, please!ģ0.9.20 I have now evaluated nine different sequencing tests - a mix of targetted Y, short, long and linked read whole genome tests. However as usual we need a lot more samples and they need to cover Scotland as well as Ireland to really make sense of the past and modern distribution. The Dublin sample being by far the oldest is the most interesting. The former two have been added to the M222 tree on and added to the M222 project there. The worst quality one is VK44 (Faroes, 16-17th C CE) which could be M222-S658 but really is lacking other markers as confirmation. Samples VK95 (Iceland 10-13th CE) and VK545 (Dublin, 665-865 CE) are confirmed members of R-M222. As usual the data quality is extremely poor but most of them can be reasonably placed on the Y tree. I have downloaded all the important raw read (BAM) files and manually examined them. The price for an entire genome sequence is very good though and reaffirms YSEQ's position as best sequencing provider not only in terms of quality but now also price.Ģ1.10.20 Raw data was recently released from the ancient Viking DNA project ( Margaryan 2019). This test was designed to give better coverage of certain kinds of variant and we will see how good it is shortly when YFull finish their analysis of my three latest kits. Oxford Nanopore long read technology is squaring off against 10X Genomics linked readsġ8.2.21 Last year the project took part in a pilot of a new 400 base pair sequencing test and this has now been officially launched by YSEQ at the cost of 335 Euros/399 USD. Kennedy (male) DNA testing DNA Overview: how THIRD Generation Sequencing (Oxford Nanopore v 10X Genomics) is revolutionising Kennedy DNA testing! (February 2021 update) ![]()
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