mpileup only calling snps for chr1 not entire genome

htetre · 06-18-2017, 10:08 AM

Hello,

I am having a problem when trying to call SNPS from two alignment files, and this also happened when I tried calling SNPs from only 1 alignment file. My problem is I am only getting SNPs for Chr01, and not for the entire genome (total Chr10).

Here is the code I am using:
samtools mpileup -B -Q 20 -P Illumina -C50 -u -f genome.fa wt_align_sorted.bam mut_align_sorted.bam | bcftools view -vcg - >var.vcf

I also have a second question in terms of the genome fasta to use. I have run the samtools faidx command on my genome and get 4 columns with 10 rows. I have tried using that output ".fai" file in the mpileup command but it does not work. Do I use the faidx file I mentioned above or the fasta file I used for mapping? When I use the fasta file I used for mapping without indexing I get SNPs but only for Chr01.

I am using Samtools v 1.3 and bcftools v 1.3

Thank you for your help

htetre · 06-20-2017, 01:56 PM

Issue was resolved for this problem. Turns out the bcftools version 1.3 uses -call instead of the older version that uses -view. And the reason it crashed after chr01 was because I did not allot enough space for it to finish.

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06-18-2017, 10:08 AM	#1
htetre Member Location: US Join Date: Jul 2013 Posts: 25	mpileup only calling snps for chr1 not entire genome Hello, I am having a problem when trying to call SNPS from two alignment files, and this also happened when I tried calling SNPs from only 1 alignment file. My problem is I am only getting SNPs for Chr01, and not for the entire genome (total Chr10). Here is the code I am using: samtools mpileup -B -Q 20 -P Illumina -C50 -u -f genome.fa wt_align_sorted.bam mut_align_sorted.bam \| bcftools view -vcg - >var.vcf I also have a second question in terms of the genome fasta to use. I have run the samtools faidx command on my genome and get 4 columns with 10 rows. I have tried using that output ".fai" file in the mpileup command but it does not work. Do I use the faidx file I mentioned above or the fasta file I used for mapping? When I use the fasta file I used for mapping without indexing I get SNPs but only for Chr01. I am using Samtools v 1.3 and bcftools v 1.3 Thank you for your help

06-20-2017, 01:56 PM	#2
htetre Member Location: US Join Date: Jul 2013 Posts: 25	issue resolved Issue was resolved for this problem. Turns out the bcftools version 1.3 uses -call instead of the older version that uses -view. And the reason it crashed after chr01 was because I did not allot enough space for it to finish.