User: linzhang

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linzhang0
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Posts by linzhang

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Comment: C: samtools mpileup and bcftools error HELP~
... Thanks a lot! (the commands were given by a senior who no longer works in our lab, I didn't know bcftools call should be used in newer version for samtools mpileup output). I generated a better .vcf file using bcftools call instead of bcftools view, however the "ID" and "FILTER" column is still "." ...
written 2.7 years ago by linzhang0
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Comment: C: samtools mpileup and bcftools error HELP~
... Thank you so much!! I tried it, it works!! but the generated .vcf file has some problems (all "" in "ALT" column, all "0" in "QUAL" column, all "." in "Filter" column). Besides, it also says "[mpileup] 1 samples in 1 input files", of which I do not know whether it is an error or not. ...
written 2.7 years ago by linzhang0
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[mpileup] 1 samples in 1 input files Is it an error?
... /samtools-1.2/samtools mpileup -d 8000 -q 25 -Iu -f reference.fasta sample.sorted.bam > sample.pileup & using the above command line gives the prompt as below:[mpileup] 1 samples in 1 input files Is it an error or I can ignore it and continue with the downstream pipeline? ...
snp written 2.7 years ago by linzhang0 • updated 9 weeks ago by Vitis1.7k
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samtools mpileup and bcftools error HELP~
... Hi I have used the below command line to call SNPs: samtools-1.2/samtools mpileup -q 25 -Iu -f reference.fasta .*.sorted.bam | bcftools view -Nv - | vcfutils.pl varFilter -Q 20 - >multicall.vcf but it gives the following error: [mpileup] 20 samples in 20 input files [bcf_sync] incorrect number ...
snp written 2.8 years ago by linzhang0 • updated 2.8 years ago by Devon Ryan86k

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