SNPs are not detected.

Question

[R]

Hi

I used bcftools to perform variant calling, but SNPs were not detected, and no SNP information was output in the VCF file. The command is as follows.

    bcftools mpileup -d 1000000 -L 1000000 -Ou -f ${REF} -a FORMAT/DP,FORMAT/AD -b bam_list.txt | bcftools call --ploidy 1 -m -v -a GQ,INFO/PV4 -o ${vcfname}_raw.vcf > ./status/mpileup.log 2>&1

Using IGVtools to examine the base composition per site, I found the following proportions:

When the ploidy is set to 1, can SNPs not be detected even if approximately 30% of the bases differ from the reference? Could you please explain why no SNPs were called at all?

Thank you

[Pierre Lindenbaum]

Could you please explain why no SNPs were called at all?

check the base quality, mapping quality, sam flags...

[R]

Thank you for your response!

I apologize for the basic question, but is it correct to check base quality, mapping quality, and SAM flags using tools like samtools view? The quality seems to be okay...

[Pierre Lindenbaum]

I apologize for the basic question, but is it correct to check base quality, mapping quality, and SAM flags using tools like samtools view?

you'd could have a look in IGV. Show us a screenshot of the alignment

[R]

Thank you for your support!

How about this? I have displayed the nucleotide composition at position 554208 and the information for the top "C". Please let me know if there is any missing information.

I would appreciate it if you could check this.

[Pierre Lindenbaum]

no idea. I suppose it's because ploidy=1