Venkatraman E. Seshan
Venkatraman E. Seshan
I am using Rsamtools v2.8.0 and pileup still double counts the overlapping section of read pairs. Can I request that it mimic the behavior of "samtools mpileup" which by default...
The high ploidy is likely due to chr15 having low allelic imbalance (logOR) while chr7q and chr9q have high logOR while at the same logR (total copy number state). Can't...
The NCBI location https://ftp.ncbi.nlm.nih.gov/snp/organisms/ only lists builds 150 and 151. How are you getting the build 153 files? You may want to see how the files dbsnp_153.hg38.vcf and 00-common_all.vcf.gz differ.
Chromosomes are named NC_000001.10 etc in build 155 (probably from 152 on). That is likely the cause.
This is a locale issue and random number seed does not have anything to do with it. If the locale is set properly you can see it with the command...
This may be a bug in emcncf. Does the naive fit show almost no change in the sample? v0.6.0 may have the bug fixed.
This is triggered by samples with no change from diploid. emcncf has been modified to catch it. This should resolve the issue without having to resort to fishing for random...
From direct messages with @makarov-ccf we found out that: …cats have three large metacentric chromosomes (A1 to A3), four large subtelomeric chromosomes (B1 to B4), two medium-size metacentrics (C1 and...
Thanks @makarov-ccf for the detailed instructions.