the limit of chromosomes

[pengyan19]

I used this cactus software and found that some smaller chromosomes do not appear in the VCF file, how can I set up all chromosomes to be output?

[glennhickey]

You might try --permissiveContigFilter (described in here) to better support tiny chromosomes.

[pengyan19]

I adjusted the value to what is appropriate, whether to adjust it up or down, I tried to adjust the value to 0.6 and 0.1, and both reduced the number of chromosomes