User: Alexander Vowinkel

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Posts by Alexander Vowinkel

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Samtools view pipe and position
... Hi, following gives the error > [main_samview] random alignment retrieval only works for indexed BAM or CRAM files. samtools merge -u -b all_files.list - | samtools view -u -q 20 -F 0x704 - '1:1-10000' > /dev/null Without the position it works. So I guess, samtools takes the position as i ...
samtools pipe written 3.9 years ago by Alexander Vowinkel0 • updated 3.9 years ago by matted7.1k
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bcf to vcf Problem
... I have downloaded the BCF of chrY from 1000G phase3: 4532c8cb3234c04e0070c00593768a90  ALL.chrY.phase3_shapeit2_mvncall_integrated.20130502.genotypes.bcf The header with hexdump looks like this: 00000000 1f 8b 08 04 00 00 00 00 00 ff 06 00 42 43 02 00 |............BC..| 00000010 36 1d ed 5d ...
bcf samtools bcftools written 4.1 years ago by Alexander Vowinkel0 • updated 4.1 years ago by alons270
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Comment: C: Bwa Mem: How To Specify The Fastq Phred Format?
... I guess you mean phred+64 to phred+33? Because phred+33 is the new one (Illumina 1.8 and Sanger) - just to prevent confusion. ...
written 4.2 years ago by Alexander Vowinkel0

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