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I have ongoing undiagnosed or only partially accounted for health problems and with a lack of family history (adoptions, absent parents etc) I have been trying to rule out genetic conditions.
I started with 23andMe before realizing how unhelpful it was. So about 10 years ago I got exome sequencing done through Genos. The main snps from 23andme matched up nicely. There was a bit of non-PAR Y chromosome data including seemingly heterozygous which lead bcftools to give ploidy as 2 for both X and Y.
The coverage was patchy even for WES so I ordered WGS from Dante Labs which took forever to return any results and the results came back with XY (I'm phenotypically female) and a het/hom ratio of 6, so reporting that to them they concluded that there "might" have been an error in quality control. Sent in a second kit and still waiting on it (not holding my breath to get any results there.)
I bit the bullet and tried Sequencing.com which had a really good turnaround time. I asked for the download link to my bam file. Their own structural variant file (called using Manta) suggested some large deletions and tandem duplications but upon viewing the bam in IGV these appear to be wildly inaccurate. Again there was a smattering of data mapped to the Y chromosome.
But to my uninformed mind the bam file looks a bit ....weird. The amount of base-pair mismatches looks really confusing. Honestly I'm quite confused and frustrated as to why I cannot seem to get a nice clear result on sequencing. Is it just bad luck? Or could there be something slightly odd about my actual DNA?
Right now I'm unsure whether to discard the whole bam file, or if it's in fact perfectly normal. The tutorials online look a lot cleaner than the data I have. For example:
I started with 23andMe before realizing how unhelpful it was. So about 10 years ago I got exome sequencing done through Genos. The main snps from 23andme matched up nicely. There was a bit of non-PAR Y chromosome data including seemingly heterozygous which lead bcftools to give ploidy as 2 for both X and Y.
The coverage was patchy even for WES so I ordered WGS from Dante Labs which took forever to return any results and the results came back with XY (I'm phenotypically female) and a het/hom ratio of 6, so reporting that to them they concluded that there "might" have been an error in quality control. Sent in a second kit and still waiting on it (not holding my breath to get any results there.)
I bit the bullet and tried Sequencing.com which had a really good turnaround time. I asked for the download link to my bam file. Their own structural variant file (called using Manta) suggested some large deletions and tandem duplications but upon viewing the bam in IGV these appear to be wildly inaccurate. Again there was a smattering of data mapped to the Y chromosome.
But to my uninformed mind the bam file looks a bit ....weird. The amount of base-pair mismatches looks really confusing. Honestly I'm quite confused and frustrated as to why I cannot seem to get a nice clear result on sequencing. Is it just bad luck? Or could there be something slightly odd about my actual DNA?
Right now I'm unsure whether to discard the whole bam file, or if it's in fact perfectly normal. The tutorials online look a lot cleaner than the data I have. For example: