Comments (3)
The reads are collected for each insertion (if longer than the insert size, then are the two tail-side reads) under tmp/cns
folder named temp_disc.sam
and temp_clip.sam
. You can split out the reads of each insertion and do a local assembly. I'll export an option for this in the next release.
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We don't have a joint genotyping module right now. Only have the gVCF level genotype. When I tried to merge them with some in-house script, if an insertion is not in a samples, I set the genotype as "0/0". I was told some tool like survivor could do the vcf merging, although I didn't try before.
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Thank you so much for your reply.
And a short question, have you ever tried merging the ME insertion sites across all the samples, and genotyping each sample for the list of merged sites? If so, what programs do you recommend me use for this?
Thank you in advance,
Best regards,
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Related Issues (20)
- output question HOT 12
- sklearn version? HOT 1
- output vcf HOT 1
- Mosaic calling - missing parameter? HOT 2
- no enough disc support! HOT 1
- Handling duplicates HOT 2
- Issue running locally HOT 1
- HERV doesn't generate .vcf and gets error while reading reads_fa folder HOT 1
- Cannot find the target directory HOT 2
- no such option: --bamsnap HOT 7
- Pre-generated Alu database HOT 1
- default slurm script with wrong email HOT 1
- -f: steps to run. (5907 means run all the steps); HOT 1
- long read support with chm13 HOT 3
- Using the code in github still doesn't solve the problem HOT 2
- Questions about the output file HOT 3
- visual inspection using IGV
- Merge clip and disc step error HOT 12
- Sporadic inconsistent errors with xtea_long HOT 5
- WES issues HOT 1
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