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Published 20 hours ago • verified publisher icon zhouzilu

BAM file from CellRanger

Open jakalssj3 opened this issue 4 years ago • 0 comments

Hello,

in the process of generating VCF file, can I use the 'possorted_genome_bam.bam' file that is returned by the CellRanger Count software? Or is it recommended to redo the mapping step?

Does the pipeline accept VCF files generated in a different way than using PicardTools and GATK, e.g. strelka2, freebayes, vartrix, or simply samtools mpileup?

jakalssj3 avatar Mar 04 '21 17:03 jakalssj3