I am having single end sequence data from Illumina and did the mapping using the Bowtie2 default parameters. Then I converted it to bam format from sam format using samtools view -bS ....sam > .......bam
Then I sorted the bam file using
samtools sort ........bam .....sorted
Then I used samtools
samtools mpileup -uf hg19.fa .......sorted.bam | bcftools view -vcg - > ......vcf
Then when I saw the result in the vcf format, I was able to see only chr 1,2,3,4,
I was not able to find the variations in rest of the chromosomes.
The data is of a human single cell.
Any idea why i got only SNPs and INDELs for first 4 chromosomes. I am not sure where I went wrong and also I have used default parameters everywhere possible.
Any ideas or answers are welcome. Thanks in advance.
Then I sorted the bam file using
samtools sort ........bam .....sorted
Then I used samtools
samtools mpileup -uf hg19.fa .......sorted.bam | bcftools view -vcg - > ......vcf
Then when I saw the result in the vcf format, I was able to see only chr 1,2,3,4,
I was not able to find the variations in rest of the chromosomes.
The data is of a human single cell.
Any idea why i got only SNPs and INDELs for first 4 chromosomes. I am not sure where I went wrong and also I have used default parameters everywhere possible.
Any ideas or answers are welcome. Thanks in advance.
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