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5.7 years ago
miqrom
•
0
Hello, I have 22 VCFs with every autosomal chromosome , all aligned with BWA MEM and UCSC GRCh37 fasta from the same fastq files (paired end). Source is a Whole Exome Sequencing x30 (illumina chip) generated with samtools/bcftools. I ran bcftools mpileup to every sorted bam and called all snp-indel variants without filtering. Finally, I merge VCFs with "bcftools merge" though I get 22 columns, one for every sorted bam source. I haven't enough RAM to merge BAM files with "samtools merge". Do you know any bcftools/vcftools command or option to group 22 columns in one?
