Hi all,
I have used samtools for variant calling with the below command: samtools mpileup -ABugf ref.fa -l target.bed -d 1000000 input.bam | bcftools view -vcg - | vcfutils.pl varFilter -D 1000000 > SAM.vcf Some variants do not have the information after column 6. Below is an example: $ grep "62105986" SAM.vcf chr2 62105986 . C T 221 I could not do further analysis with other tools because of this missing information. Could someone comment why this happens? and ways to fix this. Thanks Br Mehar ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
