User: bandanaschapagain
bandanaschapagain • 30
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Posts by bandanaschapagain
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... I found the error. It was the RG I was missing up, and it just printed header to my bam file. Now, I am able to run samtools depth. Thank you. ...
written 1 day ago by
bandanaschapagain • 30
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... -I did install latest version of samtools:
samtools --version= samtools 1.11
Using htslib 1.11
Then I tried to split the original .bam file by using one sample
samtools view -h -r Sampl1 input.bam > Sample1.bam
Then I used
samtools depth -a -H Sampl1.bam -o Sample1_bam ...
written 8 days ago by
bandanaschapagain • 30
• updated
8 days ago by
GenoMax ♦ 96k
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... Hi,
Knowing that -H option is not so important as it is for header, I just ran the code without it.
for RG in SAMPLE; do samtools view -u -r ${RG} input.bam | samtools depth -a -o {RG}.depth.txt; done
Now the error I have is:
depth: invalid option -- 'o'
Is it because of the old version of sam ...
written 9 days ago by
bandanaschapagain • 30
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... Hi @GenoMax samtools that I have is of 1.3.1 version.
I see:
samtools 1.3.1
Using htslib 1.3.1 ...
written 9 days ago by
bandanaschapagain • 30
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... Hi, I highly appreciate any help at this point. ...
written 10 days ago by
bandanaschapagain • 30
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... Hi @Pierre Lindenbaum
I did as per your suggetion, and I got the error as
depth: invalid option -- 'H'
So I changed my code to parse just one sample. But I got the same error.
My code for one sample is:
for RG in Sample1; do samtools view -u -r ${RG} input.bam | samtools depth -a -H -o {RG}.dep ...
written 10 days ago by
bandanaschapagain • 30
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... I am using samtools depth to get read depth at each position from the bam file which I have after doing alignment.
I used the command:
samtools depth -a -H input.bam -o output_duplicates
Since my bam file comprise more than one sample, how samtools depth will calculate the read depth?
The output f ...
written 13 days ago by
bandanaschapagain • 30
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Comment:
C: bcftools variant calling
... Hi, I am still not clear with what statistics bcftools used for variant calling. ...
written 27 days ago by
bandanaschapagain • 30
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... I highly appreciate any suggestion at this point. ...
written 28 days ago by
bandanaschapagain • 30
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... Hi,
I am trying to analyse my mitochondrial data set. As mitochondria are heteroplasmic and haploid, while using bcftools how can I specify both?
Earlier I used the command to call the variants to my bcf file created my using bcftools mpileup
bcftools call --ploidy 1 -m -v -o my_input_raw.bcf
I tr ...
written 29 days ago by
bandanaschapagain • 30
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