[shwetaramdas]

I was wondering if vyellappa's query was resolved? I'm getting the exact same error when I run another program that calls samtools.

Traceback (most recent call last):
File "../conifer/conifer_v0.2/conifer.py", line 597, in <module>
args.func(args)
File "../conifer/conifer_v0.2/conifer.py", line 526, in CF_bam2RPKM
iter = f.fetch(p_chr,p_start,p_stop)
File "csamtools.pyx", line 771, in csamtools.Samfile.fetch (pysam/csamtools.c:8233)
File "csamtools.pyx", line 702, in csamtools.Samfile._parseRegion (pysam/csamtools.c:7458)
ValueError: invalid reference `chr1`

Thanks!

[vyellapa]

I should have been clearer earlier.In sam fetch line:

samfile.fetch('chr1', 100, 120):

Replace 'chr1' with '1' if that's how its encoded in your bam.

[syfo]

Different read numbers between samtools view -c and pysam fetch()

Any idea why pysam.Samfile and samtools don't see the same number of reads in a bam file?

samtools view -c file.bam

=> 355.610

python
>>> import pysam
>>> bam=pysam.Samfile("file.bam")
>>> N=0
>>> for read in bam.fetch(): N+=1
... 
>>> N

=> 329.366

Thanks in advance

[syfo]

Any idea why pysam.Samfile and samtools don't see the same number of reads in a bam file?

samtools view -c file.bam

=> 355.610

python
>>> import pysam
>>> bam=pysam.Samfile("file.bam")
>>> N=0
>>> for read in bam.fetch(): N+=1
... 
>>> N

=> 329.366

Thanks in advance

Problem solved - no need to fetch:

for read in bam: N+=1

=> 355.610

[Mat29]

Can Pysam call variants on .sam files?

Can Pysam call variants on .sam files?

[dpryan]

No, more or less everything needs a sorted BAM file. I assume you're the same person who asked this in various forms on biostars too. Why not just convert to a BAM file, sort and index it? That's not exactly difficult.

[Mat29]

Please tell how to compare 300 VCF files using PySAM or smth else and to generate nonshared unique SNPs?