Limitto
Limitto
should the truncated file be called again using 'smoove call' ?
I did this but nothing was returned: for vcf in *.genotyped.vcf.gz do echo $vcf zcat $vcf | grep -v '##' | awk 'NF != 10' done Also, I was trying...
for CIPOS, CIEND, PRPOS, end PREND, I do not have samples without these tags.
I identified two samples so far, that stops the merging process, at the same position. however, they have PROPOS and PREND tags annotated correctly. Could what is annotated in these...
hmm. maybe a dumb question. but how does it matter if you have 95 , delimited values, instead of 200?
Hi, I thought I at least was able to identify samples with problem (without knowing what is the problem), but I think I was wrong. I realized that some samples...
I removed the variants that cause the merging problem. Without the problem variants, merging goes smoothly. Would you be interested in having a look? I can send you the vcf...
Hello, Thanks for the quick answer! When I checked the MAPQ>20, I see 2 discordant read pairs.  Do you think these are sufficient to call a duplication? In my...
Hi again, I found a sample that has three discordant read pairs with high MAPQ (both forward and reverse reads MAPQ >50). So, I ran Smoove call with -support 1,...
That is a pity. Because the orientation of the reads must be interpreted as a duplication. Also, the reads seem to be clustered well...although there is no split-reads support (because...