Do other species that adopt the 1a pattern need to specify chromosomes

[qiqi277]

Hello, can I specify chromosomes in mode 1a? I want to detect all the chromosomes of pigs, but only 18 autosomes can be detected in the vcf file generated by running mode 1a. How can I detect X, Y and MT together? Here are the commands to run.

#mode1	 
$cellsnp -s $BAM -b $BARCODE -O $output -R $REGION_VCF -p 10 --minMAF 0.1 --minCOUNT 20 --gzip --genotype \
     --chrom 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,X,Y,MT && echo " cellsnp completed." || echo "cellsnp failed."

Looking forward to your reply, I would appreciate it

[hxj5]

Hi, the --chrom option will be ignored in mode 1a.

The outputted SNPs of mode 1a depends on the input SNPs specified by -R, hence you may need to include the SNPs of chromosome 'X', 'Y', 'MT' in the input VCF. Here I assume the VCF contains pig SNPs instead of human SNPs.