samtools mpileup output file format?

[dkrtndhkd]

at first, I install samtools by ubuntu software center. samtools of old version.

when i command 'samtools pileup -vcf ref.fasta aln.sorted.bam > aln_result'

then samtools make aln_result file and it shows the raw indel/snp information which is not corresponding reference.


i reinstalled ubuntu and i installed samtools by downloading from sourceforge.net(latest version)

as you know, 'pileup' option is deprecated and replaced with 'mpileup' option.

I just followed 'Manual Reference Pages - samtools', my command line is like this;

samtools mpileup -C50 -gf ref.fasta aln.sorted.bam > file1(it's compressed binary file)
bcftools index file1
bcftools view file1 chr*:****-**** > out.vcf
bcftools view -vc file1 > out.vcf 2 > out.afs

I couldn't open file1 because it's binary format and out.vcf shows snp/indel but cannot recognize ref.fasta so only dot('.') is shown at the REF column.

where am i wrong?(reference file is absolutely normal as i know. when i use tview option, the reference sequence is shown well)

is it right to input file1 to in.bcf at using bcftools?

[dpryan]

The file you posted has the reference column filled in and an X in the ALT column, presumably due to the low depth. There are dots in the ID and FILTER fields

[dkrtndhkd]

Ah......!!! oh my eyes...^^;;

thank you!!! and another question...

what should i do for it?

you said X in the ALT column due to the low depth, but what should the samtool's standard for judgement be?

as i know, at some position, it has depth bigger than 100X...

[Ekeberg]

dkrtndhkd I have the same problem. How did you fixed it?